PDB Short entry for 4ZDV HEADER PROTEIN TRANSPORT 19-APR-15 4ZDV TITLE CRYSTAL STRUCTURE OF LC3 IN COMPLEX WITH FAM134B LIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUTOPHAGY-RELATED PROTEIN LC3 A,AUTOPHAGY-RELATED UBIQUITIN- COMPND 5 LIKE MODIFIER LC3 A,MAP1 LIGHT CHAIN 3-LIKE PROTEIN 1,MAP1A/MAP1B COMPND 6 LIGHT CHAIN 3 A,MAP1A/MAP1B LC3 A,MICROTUBULE-ASSOCIATED PROTEIN 1 COMPND 7 LIGHT CHAIN 3 ALPHA; COMPND 8 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: MAP1LC3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AUTOPHAGY, ER-PHAGY, COMPLEX, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.KHAMINETS,P.GRUMATI,I.DIKIC,M.AKUTSU REVDAT 4 10-JAN-24 4ZDV 1 ATOM REVDAT 3 24-JUN-15 4ZDV 1 JRNL REVDAT 2 17-JUN-15 4ZDV 1 JRNL REVDAT 1 03-JUN-15 4ZDV 0 JRNL AUTH A.KHAMINETS,T.HEINRICH,M.MARI,P.GRUMATI,A.K.HUEBNER, JRNL AUTH 2 M.AKUTSU,L.LIEBMANN,A.STOLZ,S.NIETZSCHE,N.KOCH,M.MAUTHE, JRNL AUTH 3 I.KATONA,B.QUALMANN,J.WEIS,F.REGGIORI,I.KURTH,C.A.HUBNER, JRNL AUTH 4 I.DIKIC JRNL TITL REGULATION OF ENDOPLASMIC RETICULUM TURNOVER BY SELECTIVE JRNL TITL 2 AUTOPHAGY. JRNL REF NATURE V. 522 354 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26040720 JRNL DOI 10.1038/NATURE14498 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14088 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 701 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 47.7260 - 3.0779 1.00 2850 141 0.1705 0.2105 REMARK 3 2 3.0779 - 2.4430 1.00 2681 131 0.2065 0.2482 REMARK 3 3 2.4430 - 2.1342 1.00 2623 152 0.1861 0.2095 REMARK 3 4 2.1342 - 1.9391 1.00 2626 136 0.1901 0.2185 REMARK 3 5 1.9391 - 1.8001 1.00 2607 141 0.2045 0.2626 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.72 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 1067 REMARK 3 ANGLE : 1.069 1439 REMARK 3 CHIRALITY : 0.090 156 REMARK 3 PLANARITY : 0.005 190 REMARK 3 DIHEDRAL : 14.127 419 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): 21.0685 -10.5138 14.5465 REMARK 3 T TENSOR REMARK 3 T11: 0.1189 T22: 0.1680 REMARK 3 T33: 0.1507 T12: -0.0094 REMARK 3 T13: 0.0137 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.4820 L22: 0.7421 REMARK 3 L33: 1.1082 L12: -0.0402 REMARK 3 L13: 0.3345 L23: 0.0742 REMARK 3 S TENSOR REMARK 3 S11: 0.0565 S12: -0.0356 S13: -0.1539 REMARK 3 S21: -0.0245 S22: -0.0040 S23: -0.1293 REMARK 3 S31: 0.1371 S32: -0.0924 S33: -0.0547 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 4ZDV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14123 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 62.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3ECI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% TACSIMATE (HAMPTON RESEARCH) PH REMARK 280 8.0, 20% POLY ETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.08500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.20500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.08500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.08500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.20500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.08500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.08500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.20500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.08500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.08500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.20500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 274 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 282 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 312 LIES ON A SPECIAL POSITION. 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 -11 REMARK 465 PRO A -10 REMARK 465 GLU A -9 REMARK 465 GLU A -8 REMARK 465 GLY A -7 REMARK 465 GLY A 120 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN A 116 O HOH A 201 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 85 14.18 54.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 4ZDV A 2 120 UNP Q9H492 MLP3A_HUMAN 2 120 SEQADV 4ZDV GLY A -11 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV PRO A -10 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV GLU A -9 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV GLU A -8 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV GLY A -7 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV ASP A -6 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV ASP A -5 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV PHE A -4 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV GLU A -3 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV LEU A -2 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV LEU A -1 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV ASP A 0 UNP Q9H492 EXPRESSION TAG SEQADV 4ZDV GLY A 1 UNP Q9H492 EXPRESSION TAG SEQRES 1 A 132 GLY PRO GLU GLU GLY ASP ASP PHE GLU LEU LEU ASP GLY SEQRES 2 A 132 PRO SER ASP ARG PRO PHE LYS GLN ARG ARG SER PHE ALA SEQRES 3 A 132 ASP ARG CYS LYS GLU VAL GLN GLN ILE ARG ASP GLN HIS SEQRES 4 A 132 PRO SER LYS ILE PRO VAL ILE ILE GLU ARG TYR LYS GLY SEQRES 5 A 132 GLU LYS GLN LEU PRO VAL LEU ASP LYS THR LYS PHE LEU SEQRES 6 A 132 VAL PRO ASP HIS VAL ASN MET SER GLU LEU VAL LYS ILE SEQRES 7 A 132 ILE ARG ARG ARG LEU GLN LEU ASN PRO THR GLN ALA PHE SEQRES 8 A 132 PHE LEU LEU VAL ASN GLN HIS SER MET VAL SER VAL SER SEQRES 9 A 132 THR PRO ILE ALA ASP ILE TYR GLU GLN GLU LYS ASP GLU SEQRES 10 A 132 ASP GLY PHE LEU TYR MET VAL TYR ALA SER GLN GLU THR SEQRES 11 A 132 PHE GLY FORMUL 2 HOH *116(H2 O) HELIX 1 AA1 GLY A 1 ARG A 5 5 5 HELIX 2 AA2 PRO A 6 ARG A 11 1 6 HELIX 3 AA3 SER A 12 HIS A 27 1 16 HELIX 4 AA4 ASN A 59 LEU A 71 1 13 HELIX 5 AA5 PRO A 94 LYS A 103 1 10 SHEET 1 AA1 5 LYS A 51 PRO A 55 0 SHEET 2 AA1 5 LYS A 30 ARG A 37 -1 N ILE A 31 O VAL A 54 SHEET 3 AA1 5 LEU A 109 ALA A 114 1 O MET A 111 N ILE A 34 SHEET 4 AA1 5 PHE A 80 VAL A 83 -1 N LEU A 82 O VAL A 112 SHEET 5 AA1 5 HIS A 86 SER A 87 -1 O HIS A 86 N VAL A 83 CRYST1 62.170 62.170 74.410 90.00 90.00 90.00 P 42 21 2 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 0.016085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013439 0.00000