PDB Short entry for 5WWX HEADER RNA BINDING PROTEIN/RNA 05-JAN-17 5WWX TITLE CRYSTAL STRUCTURE OF THE KH2 DOMAIN OF HUMAN RNA-BINDING E3 UBIQUITIN- TITLE 2 PROTEIN LIGASE MEX-3C COMPLEX WITH RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING E3 UBIQUITIN-PROTEIN LIGASE MEX3C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KH2 DOMAIN, UNP RESIDUES 320-396; COMPND 5 SYNONYM: RING FINGER AND KH DOMAIN-CONTAINING PROTEIN 2,RING FINGER COMPND 6 PROTEIN 194,RING-TYPE E3 UBIQUITIN TRANSFERASE MEX3C; COMPND 7 EC: 2.3.2.27; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (5'-R(P*AP*GP*AP*GP*U)-3'); COMPND 11 CHAIN: C; 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: MEX3C, RKHD2, RNF194, BM-013; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS KH2, MEX-3C, RNA, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.YANG,C.WANG,F.LI,Q.GONG REVDAT 4 22-NOV-23 5WWX 1 LINK REVDAT 3 11-OCT-17 5WWX 1 JRNL REVDAT 2 30-AUG-17 5WWX 1 REMARK REVDAT 1 23-AUG-17 5WWX 0 JRNL AUTH L.YANG,C.WANG,F.LI,J.ZHANG,A.NAYAB,J.WU,Y.SHI,Q.GONG JRNL TITL THE HUMAN RNA-BINDING PROTEIN AND E3 LIGASE MEX-3C BINDS THE JRNL TITL 2 MEX-3-RECOGNITION ELEMENT (MRE) MOTIF WITH HIGH AFFINITY JRNL REF J. BIOL. CHEM. V. 292 16221 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28808060 JRNL DOI 10.1074/JBC.M117.797746 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 6586 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 337 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 33.3717 - 2.5187 0.99 3195 171 0.1698 0.2041 REMARK 3 2 2.5187 - 1.9992 1.00 3054 166 0.1707 0.2521 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.09 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 : 0.008 848 REMARK 3 ANGLE : 0.923 1179 REMARK 3 CHIRALITY : 0.051 133 REMARK 3 PLANARITY : 0.005 137 REMARK 3 DIHEDRAL : 16.630 508 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5WWX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300002533. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL-2000, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6609 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.53400 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: PHASER REMARK 200 STARTING MODEL: 5WWW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.05M SODIUM CACODYLATE TRIHYDRATE PH 6.0, 30% V/V (+/-)-2- REMARK 280 METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 16.26750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.30550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.30550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.40125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.30550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.30550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.13375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.30550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.30550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.40125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.30550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.30550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 8.13375 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 16.26750 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 NI NI A 401 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 548 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 MET A 311 REMARK 465 GLY A 312 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 505 O HOH A 505 8666 2.10 REMARK 500 O HOH A 515 O HOH C 113 1556 2.19 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 ASP A 366 40.55 -104.69 REMARK 500 REMARK 500 REMARK: NULL 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 NI A 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 314 NE2 REMARK 620 2 HIS A 314 NE2 0.0 REMARK 620 3 HIS A 316 NE2 102.5 102.5 REMARK 620 4 HIS A 316 NE2 102.5 102.5 0.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WWW RELATED DB: PDB REMARK 900 RELATED ID: 5WWZ RELATED DB: PDB DBREF 5WWX A 320 396 UNP Q5U5Q3 MEX3C_HUMAN 320 396 DBREF 5WWX C 1 5 PDB 5WWX 5WWX 1 5 SEQADV 5WWX MET A 311 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX GLY A 312 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX HIS A 313 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX HIS A 314 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX HIS A 315 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX HIS A 316 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX HIS A 317 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX HIS A 318 UNP Q5U5Q3 EXPRESSION TAG SEQADV 5WWX MET A 319 UNP Q5U5Q3 EXPRESSION TAG SEQRES 1 A 86 MET GLY HIS HIS HIS HIS HIS HIS MET SER PRO ASN LEU SEQRES 2 A 86 PRO GLY GLN THR THR VAL GLN VAL ARG VAL PRO TYR ARG SEQRES 3 A 86 VAL VAL GLY LEU VAL VAL GLY PRO LYS GLY ALA THR ILE SEQRES 4 A 86 LYS ARG ILE GLN GLN GLN THR HIS THR TYR ILE VAL THR SEQRES 5 A 86 PRO SER ARG ASP LYS GLU PRO VAL PHE GLU VAL THR GLY SEQRES 6 A 86 MET PRO GLU ASN VAL ASP ARG ALA ARG GLU GLU ILE GLU SEQRES 7 A 86 MET HIS ILE ALA MET ARG THR GLY SEQRES 1 C 5 A G A G U HET NI A 401 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI NI 2+ FORMUL 4 HOH *62(H2 O) HELIX 1 AA1 PRO A 334 ARG A 336 5 3 HELIX 2 AA2 VAL A 337 GLY A 343 1 7 HELIX 3 AA3 GLY A 346 HIS A 357 1 12 HELIX 4 AA4 MET A 376 GLY A 396 1 21 SHEET 1 AA1 3 THR A 327 ARG A 332 0 SHEET 2 AA1 3 VAL A 370 GLY A 375 -1 O PHE A 371 N VAL A 331 SHEET 3 AA1 3 TYR A 359 VAL A 361 -1 N TYR A 359 O THR A 374 LINK NE2 HIS A 314 NI NI A 401 1555 1555 1.98 LINK NE2 HIS A 314 NI NI A 401 1555 7555 1.98 LINK NE2 HIS A 316 NI NI A 401 1555 1555 2.07 LINK NE2 HIS A 316 NI NI A 401 1555 7555 2.07 SITE 1 AC1 2 HIS A 314 HIS A 316 CRYST1 74.611 74.611 32.535 90.00 90.00 90.00 P 43 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 0.013403 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013403 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030736 0.00000