PDB Short entry for 6RIR HEADER SIGNALING PROTEIN 25-APR-19 6RIR TITLE CRYSTAL STRUCTURE OF PHOSPHORYLATED RAB8A IN COMPLEX WITH THE RAB- TITLE 2 BINDING DOMAIN OF RILPL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-8A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ONCOGENE C-MEL; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RILP-LIKE PROTEIN 2; COMPND 9 CHAIN: D, C; COMPND 10 SYNONYM: RAB-INTERACTING LYSOSOMAL PROTEIN-LIKE 2,P40PHOX-BINDING COMPND 11 PROTEIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB8A, MEL, RAB8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RILPL2, RLP2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE TRAFFICKING, RAB GTPASE, EFFECTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.WASCHBUSCH,E.PURLYTE,D.R.ALESSI,A.R.KHAN REVDAT 5 24-JAN-24 6RIR 1 LINK REVDAT 4 15-APR-20 6RIR 1 JRNL REVDAT 3 19-FEB-20 6RIR 1 JRNL REVDAT 2 12-FEB-20 6RIR 1 AUTHOR REVDAT 1 29-JAN-20 6RIR 0 JRNL AUTH D.WASCHBUSCH,E.PURLYTE,P.PAL,E.MCGRATH,D.R.ALESSI,A.R.KHAN JRNL TITL STRUCTURAL BASIS FOR RAB8A RECRUITMENT OF RILPL2 VIA LRRK2 JRNL TITL 2 PHOSPHORYLATION OF SWITCH 2. JRNL REF STRUCTURE V. 28 406 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 32017888 JRNL DOI 10.1016/J.STR.2020.01.005 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.WASCHBUSCH,E.PURLYTE,P.PAL,E.MCGRATH,D.R.ALESSI,A.R.KHAN REMARK 1 TITL STRUCTURAL BASIS FOR RAB8A GTPASE RECRUITMENT OF RILPL2 VIA REMARK 1 TITL 2 LRRK2-MEDIATED PHOSPHORYLATION OF SWITCH 2 REMARK 1 REF STRUCTURE 2020 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.2139/SSRN.3451451 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 93460 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 4587 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 60.7302 - 5.4891 1.00 2939 163 0.1894 0.1961 REMARK 3 2 5.4891 - 4.3573 1.00 2980 162 0.1486 0.1698 REMARK 3 3 4.3573 - 3.8066 1.00 2982 156 0.1415 0.1773 REMARK 3 4 3.8066 - 3.4586 1.00 2969 164 0.1517 0.1943 REMARK 3 5 3.4586 - 3.2107 1.00 2961 169 0.1620 0.1985 REMARK 3 6 3.2107 - 3.0214 1.00 2977 121 0.1665 0.2285 REMARK 3 7 3.0214 - 2.8701 1.00 3033 135 0.1722 0.2107 REMARK 3 8 2.8701 - 2.7452 1.00 2913 180 0.1798 0.1930 REMARK 3 9 2.7452 - 2.6395 1.00 3033 120 0.1744 0.2045 REMARK 3 10 2.6395 - 2.5484 1.00 2976 144 0.1845 0.2012 REMARK 3 11 2.5484 - 2.4687 1.00 3008 133 0.1963 0.2841 REMARK 3 12 2.4687 - 2.3981 1.00 2974 154 0.1795 0.2085 REMARK 3 13 2.3981 - 2.3350 1.00 2969 174 0.1781 0.2101 REMARK 3 14 2.3350 - 2.2780 1.00 2946 173 0.1828 0.1904 REMARK 3 15 2.2780 - 2.2262 1.00 2996 148 0.1880 0.2200 REMARK 3 16 2.2262 - 2.1789 1.00 2985 129 0.1870 0.2305 REMARK 3 17 2.1789 - 2.1353 1.00 2980 156 0.1902 0.1990 REMARK 3 18 2.1353 - 2.0950 1.00 2962 167 0.1906 0.2443 REMARK 3 19 2.0950 - 2.0576 1.00 2976 159 0.2026 0.2422 REMARK 3 20 2.0576 - 2.0227 1.00 3021 141 0.2086 0.2716 REMARK 3 21 2.0227 - 1.9901 1.00 2921 142 0.2106 0.2407 REMARK 3 22 1.9901 - 1.9594 1.00 3020 146 0.2372 0.2750 REMARK 3 23 1.9594 - 1.9306 1.00 2946 159 0.2362 0.2714 REMARK 3 24 1.9306 - 1.9034 1.00 3016 154 0.2573 0.3069 REMARK 3 25 1.9034 - 1.8777 1.00 2903 162 0.2588 0.2983 REMARK 3 26 1.8777 - 1.8533 1.00 2997 165 0.2525 0.2473 REMARK 3 27 1.8533 - 1.8301 1.00 2920 149 0.2623 0.2841 REMARK 3 28 1.8301 - 1.8081 1.00 3063 145 0.2679 0.2484 REMARK 3 29 1.8081 - 1.7871 1.00 2933 162 0.2901 0.3267 REMARK 3 30 1.7871 - 1.7670 0.87 2574 155 0.3048 0.3358 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3524 REMARK 3 ANGLE : 0.912 4744 REMARK 3 CHIRALITY : 0.056 524 REMARK 3 PLANARITY : 0.004 590 REMARK 3 DIHEDRAL : 11.146 2827 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 21.0632 29.7642 -6.1688 REMARK 3 T TENSOR REMARK 3 T11: 0.1756 T22: 0.2322 REMARK 3 T33: 0.1864 T12: -0.0026 REMARK 3 T13: 0.0181 T23: -0.0346 REMARK 3 L TENSOR REMARK 3 L11: 0.1937 L22: 1.7405 REMARK 3 L33: 0.2637 L12: -0.1648 REMARK 3 L13: 0.0626 L23: -0.3953 REMARK 3 S TENSOR REMARK 3 S11: 0.0061 S12: -0.0132 S13: 0.0188 REMARK 3 S21: -0.0758 S22: 0.0097 S23: -0.0703 REMARK 3 S31: -0.0169 S32: 0.0112 S33: -0.0084 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6RIR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49201 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.767 REMARK 200 RESOLUTION RANGE LOW (A) : 53.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06877 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.94880 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.690 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4LHW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8K 100MM NA HEPES, PH 7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.16650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.39200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.75450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.39200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.16650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.75450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 LEU A 177 REMARK 465 GLU A 178 REMARK 465 GLY A 179 REMARK 465 ASN A 180 REMARK 465 SER A 181 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 LEU B 177 REMARK 465 GLU B 178 REMARK 465 GLY B 179 REMARK 465 ASN B 180 REMARK 465 SER B 181 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 HIS D 127 REMARK 465 HIS D 128 REMARK 465 CYS D 161 REMARK 465 TYR D 162 REMARK 465 LYS D 163 REMARK 465 SER D 164 REMARK 465 GLY D 165 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 HIS C 125 REMARK 465 HIS C 126 REMARK 465 HIS C 127 REMARK 465 GLN C 160 REMARK 465 CYS C 161 REMARK 465 TYR C 162 REMARK 465 LYS C 163 REMARK 465 SER C 164 REMARK 465 GLY C 165 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG D 132 -33.88 -134.83 REMARK 500 LEU D 159 61.74 -101.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 462 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 463 DISTANCE = 5.84 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 THR A 40 OG1 83.7 REMARK 620 3 GTP A 201 O3G 173.8 91.4 REMARK 620 4 GTP A 201 O2B 91.7 175.4 93.2 REMARK 620 5 HOH A 315 O 86.6 91.1 97.2 89.0 REMARK 620 6 HOH A 356 O 87.6 91.1 88.9 88.3 173.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 22 OG1 REMARK 620 2 THR B 40 OG1 84.6 REMARK 620 3 GTP B 900 O3G 174.8 91.4 REMARK 620 4 GTP B 900 O2B 90.3 174.5 93.5 REMARK 620 5 HOH B1017 O 86.8 89.9 89.8 87.8 REMARK 620 6 HOH B1053 O 87.3 93.2 96.2 88.6 173.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP B 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 901 DBREF 6RIR A 1 181 UNP P61006 RAB8A_HUMAN 1 181 DBREF 6RIR B 1 181 UNP P61006 RAB8A_HUMAN 1 181 DBREF 6RIR D 129 165 UNP Q969X0 RIPL2_HUMAN 129 165 DBREF 6RIR C 129 165 UNP Q969X0 RIPL2_HUMAN 129 165 SEQADV 6RIR GLY A -2 UNP P61006 EXPRESSION TAG SEQADV 6RIR SER A -1 UNP P61006 EXPRESSION TAG SEQADV 6RIR HIS A 0 UNP P61006 EXPRESSION TAG SEQADV 6RIR LEU A 67 UNP P61006 GLN 67 ENGINEERED MUTATION SEQADV 6RIR GLY B -2 UNP P61006 EXPRESSION TAG SEQADV 6RIR SER B -1 UNP P61006 EXPRESSION TAG SEQADV 6RIR HIS B 0 UNP P61006 EXPRESSION TAG SEQADV 6RIR LEU B 67 UNP P61006 GLN 67 ENGINEERED MUTATION SEQADV 6RIR HIS D 123 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS D 124 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS D 125 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS D 126 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS D 127 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS D 128 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS C 123 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS C 124 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS C 125 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS C 126 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS C 127 UNP Q969X0 EXPRESSION TAG SEQADV 6RIR HIS C 128 UNP Q969X0 EXPRESSION TAG SEQRES 1 A 184 GLY SER HIS MET ALA LYS THR TYR ASP TYR LEU PHE LYS SEQRES 2 A 184 LEU LEU LEU ILE GLY ASP SER GLY VAL GLY LYS THR CYS SEQRES 3 A 184 VAL LEU PHE ARG PHE SER GLU ASP ALA PHE ASN SER THR SEQRES 4 A 184 PHE ILE SER THR ILE GLY ILE ASP PHE LYS ILE ARG THR SEQRES 5 A 184 ILE GLU LEU ASP GLY LYS ARG ILE LYS LEU GLN ILE TRP SEQRES 6 A 184 ASP THR ALA GLY LEU GLU ARG PHE ARG TPO ILE THR THR SEQRES 7 A 184 ALA TYR TYR ARG GLY ALA MET GLY ILE MET LEU VAL TYR SEQRES 8 A 184 ASP ILE THR ASN GLU LYS SER PHE ASP ASN ILE ARG ASN SEQRES 9 A 184 TRP ILE ARG ASN ILE GLU GLU HIS ALA SER ALA ASP VAL SEQRES 10 A 184 GLU LYS MET ILE LEU GLY ASN LYS CYS ASP VAL ASN ASP SEQRES 11 A 184 LYS ARG GLN VAL SER LYS GLU ARG GLY GLU LYS LEU ALA SEQRES 12 A 184 LEU ASP TYR GLY ILE LYS PHE MET GLU THR SER ALA LYS SEQRES 13 A 184 ALA ASN ILE ASN VAL GLU ASN ALA PHE PHE THR LEU ALA SEQRES 14 A 184 ARG ASP ILE LYS ALA LYS MET ASP LYS LYS LEU GLU GLY SEQRES 15 A 184 ASN SER SEQRES 1 B 184 GLY SER HIS MET ALA LYS THR TYR ASP TYR LEU PHE LYS SEQRES 2 B 184 LEU LEU LEU ILE GLY ASP SER GLY VAL GLY LYS THR CYS SEQRES 3 B 184 VAL LEU PHE ARG PHE SER GLU ASP ALA PHE ASN SER THR SEQRES 4 B 184 PHE ILE SER THR ILE GLY ILE ASP PHE LYS ILE ARG THR SEQRES 5 B 184 ILE GLU LEU ASP GLY LYS ARG ILE LYS LEU GLN ILE TRP SEQRES 6 B 184 ASP THR ALA GLY LEU GLU ARG PHE ARG TPO ILE THR THR SEQRES 7 B 184 ALA TYR TYR ARG GLY ALA MET GLY ILE MET LEU VAL TYR SEQRES 8 B 184 ASP ILE THR ASN GLU LYS SER PHE ASP ASN ILE ARG ASN SEQRES 9 B 184 TRP ILE ARG ASN ILE GLU GLU HIS ALA SER ALA ASP VAL SEQRES 10 B 184 GLU LYS MET ILE LEU GLY ASN LYS CYS ASP VAL ASN ASP SEQRES 11 B 184 LYS ARG GLN VAL SER LYS GLU ARG GLY GLU LYS LEU ALA SEQRES 12 B 184 LEU ASP TYR GLY ILE LYS PHE MET GLU THR SER ALA LYS SEQRES 13 B 184 ALA ASN ILE ASN VAL GLU ASN ALA PHE PHE THR LEU ALA SEQRES 14 B 184 ARG ASP ILE LYS ALA LYS MET ASP LYS LYS LEU GLU GLY SEQRES 15 B 184 ASN SER SEQRES 1 D 43 HIS HIS HIS HIS HIS HIS ASN ARG PRO ARG PHE THR LEU SEQRES 2 D 43 GLN GLU LEU ARG ASP VAL LEU GLN GLU ARG ASN LYS LEU SEQRES 3 D 43 LYS SER GLN LEU LEU VAL VAL GLN GLU GLU LEU GLN CYS SEQRES 4 D 43 TYR LYS SER GLY SEQRES 1 C 43 HIS HIS HIS HIS HIS HIS ASN ARG PRO ARG PHE THR LEU SEQRES 2 C 43 GLN GLU LEU ARG ASP VAL LEU GLN GLU ARG ASN LYS LEU SEQRES 3 C 43 LYS SER GLN LEU LEU VAL VAL GLN GLU GLU LEU GLN CYS SEQRES 4 C 43 TYR LYS SER GLY MODRES 6RIR TPO A 72 THR MODIFIED RESIDUE MODRES 6RIR TPO B 72 THR MODIFIED RESIDUE HET TPO A 72 11 HET TPO B 72 11 HET GTP A 201 32 HET MG A 202 1 HET GOL A 203 6 HET GTP B 900 32 HET MG B 901 1 HETNAM TPO PHOSPHOTHREONINE HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN TPO PHOSPHONOTHREONINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 TPO 2(C4 H10 N O6 P) FORMUL 5 GTP 2(C10 H16 N5 O14 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 10 HOH *353(H2 O) HELIX 1 AA1 GLY A 20 ASP A 31 1 12 HELIX 2 AA2 LEU A 67 ARG A 69 5 3 HELIX 3 AA3 PHE A 70 ALA A 76 1 7 HELIX 4 AA4 ASN A 92 ASN A 98 1 7 HELIX 5 AA5 ASN A 98 ALA A 110 1 13 HELIX 6 AA6 VAL A 125 ARG A 129 5 5 HELIX 7 AA7 SER A 132 GLY A 144 1 13 HELIX 8 AA8 ASN A 157 LYS A 175 1 19 HELIX 9 AA9 GLY B 20 ASP B 31 1 12 HELIX 10 AB1 LEU B 67 ARG B 69 5 3 HELIX 11 AB2 PHE B 70 ALA B 76 1 7 HELIX 12 AB3 ASN B 92 ASN B 98 1 7 HELIX 13 AB4 ASN B 98 ALA B 110 1 13 HELIX 14 AB5 VAL B 125 ARG B 129 5 5 HELIX 15 AB6 SER B 132 GLY B 144 1 13 HELIX 16 AB7 ASN B 157 LYS B 176 1 20 HELIX 17 AB8 THR D 134 GLU D 158 1 25 HELIX 18 AB9 THR C 134 GLU C 158 1 25 SHEET 1 AA1 6 ILE A 43 LEU A 52 0 SHEET 2 AA1 6 LYS A 55 THR A 64 -1 O ASP A 63 N ASP A 44 SHEET 3 AA1 6 TYR A 7 ILE A 14 1 N LEU A 11 O TRP A 62 SHEET 4 AA1 6 GLY A 83 ASP A 89 1 O MET A 85 N LEU A 12 SHEET 5 AA1 6 GLU A 115 ASN A 121 1 O MET A 117 N LEU A 86 SHEET 6 AA1 6 LYS A 146 GLU A 149 1 O LYS A 146 N ILE A 118 SHEET 1 AA2 6 ILE B 43 LEU B 52 0 SHEET 2 AA2 6 LYS B 55 THR B 64 -1 O ILE B 57 N ILE B 50 SHEET 3 AA2 6 TYR B 7 GLY B 15 1 N LEU B 11 O TRP B 62 SHEET 4 AA2 6 GLY B 83 ASP B 89 1 O MET B 85 N LEU B 12 SHEET 5 AA2 6 GLU B 115 ASN B 121 1 O MET B 117 N LEU B 86 SHEET 6 AA2 6 LYS B 146 GLU B 149 1 O LYS B 146 N ILE B 118 LINK C ARG A 71 N TPO A 72 1555 1555 1.33 LINK C TPO A 72 N ILE A 73 1555 1555 1.33 LINK C ARG B 71 N TPO B 72 1555 1555 1.33 LINK C TPO B 72 N ILE B 73 1555 1555 1.33 LINK OG1 THR A 22 MG MG A 202 1555 1555 2.09 LINK OG1 THR A 40 MG MG A 202 1555 1555 2.10 LINK O3G GTP A 201 MG MG A 202 1555 1555 2.01 LINK O2B GTP A 201 MG MG A 202 1555 1555 2.04 LINK MG MG A 202 O HOH A 315 1555 1555 2.14 LINK MG MG A 202 O HOH A 356 1555 1555 2.16 LINK OG1 THR B 22 MG MG B 901 1555 1555 2.10 LINK OG1 THR B 40 MG MG B 901 1555 1555 2.09 LINK O3G GTP B 900 MG MG B 901 1555 1555 2.00 LINK O2B GTP B 900 MG MG B 901 1555 1555 2.05 LINK MG MG B 901 O HOH B1017 1555 1555 2.11 LINK MG MG B 901 O HOH B1053 1555 1555 2.18 SITE 1 AC1 30 SER A 17 GLY A 18 VAL A 19 GLY A 20 SITE 2 AC1 30 LYS A 21 THR A 22 CYS A 23 PHE A 33 SITE 3 AC1 30 ASN A 34 SER A 35 THR A 36 PHE A 37 SITE 4 AC1 30 SER A 39 THR A 40 GLY A 66 ASN A 121 SITE 5 AC1 30 LYS A 122 ASP A 124 VAL A 125 SER A 151 SITE 6 AC1 30 ALA A 152 LYS A 153 MG A 202 HOH A 315 SITE 7 AC1 30 HOH A 329 HOH A 356 HOH A 362 HOH A 382 SITE 8 AC1 30 HOH A 397 HOH A 401 SITE 1 AC2 5 THR A 22 THR A 40 GTP A 201 HOH A 315 SITE 2 AC2 5 HOH A 356 SITE 1 AC3 7 LYS A 10 ASN A 34 THR A 36 TYR A 77 SITE 2 AC3 7 GLY A 80 ALA A 81 HOH A 392 SITE 1 AC4 27 SER B 17 GLY B 18 VAL B 19 GLY B 20 SITE 2 AC4 27 LYS B 21 THR B 22 CYS B 23 PHE B 33 SITE 3 AC4 27 ASN B 34 SER B 35 PHE B 37 SER B 39 SITE 4 AC4 27 THR B 40 GLY B 66 ASN B 121 LYS B 122 SITE 5 AC4 27 ASP B 124 VAL B 125 SER B 151 ALA B 152 SITE 6 AC4 27 LYS B 153 MG B 901 HOH B1017 HOH B1037 SITE 7 AC4 27 HOH B1053 HOH B1065 HOH B1087 SITE 1 AC5 5 THR B 22 THR B 40 GTP B 900 HOH B1017 SITE 2 AC5 5 HOH B1053 CRYST1 60.333 71.509 114.784 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008712 0.00000