HEADER SIGNALING PROTEIN 12-MAR-24 9B12 TITLE STRUCTURE OF OPTINEURIN BOUND TO HOIP NZF1 DOMAIN AND M1-LINKED TITLE 2 DIUBIQUITIN, CRYSTAL FORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OPTINEURIN; COMPND 3 CHAIN: C, D, E, F; COMPND 4 SYNONYM: E3-14.7K-INTERACTING PROTEIN,FIP-2,HUNTINGTIN YEAST PARTNER COMPND 5 L,HUNTINGTIN-INTERACTING PROTEIN 7,HIP-7,HUNTINGTIN-INTERACTING COMPND 6 PROTEIN L,NEMO-RELATED PROTEIN,OPTIC NEUROPATHY-INDUCING PROTEIN, COMPND 7 TRANSCRIPTION FACTOR IIIA-INTERACTING PROTEIN,TFIIIA-INTP; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: INITIAL GP SEQUENCE FROM CLONING TAG; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: UBIQUITIN; COMPND 12 CHAIN: A, B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF31; COMPND 16 CHAIN: G, H, I, J; COMPND 17 SYNONYM: HOIL-1-INTERACTING PROTEIN,HOIP,RING FINGER PROTEIN 31,RING- COMPND 18 TYPE E3 UBIQUITIN TRANSFERASE RNF31,ZINC IN-BETWEEN-RING-FINGER COMPND 19 UBIQUITIN-ASSOCIATED DOMAIN PROTEIN; COMPND 20 EC: 2.3.2.31; COMPND 21 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: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP; 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: UBB; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: RNF31, ZIBRA; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OPTINEURIN, AUTOPHAGY, MITOPHAGY, XENOPHAGY, UBAN, NZF, HOIP, LUBAC, KEYWDS 2 LINEAR UB CHAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.MICHEL,S.SCUTTS,D.KOMANDER REVDAT 1 31-JUL-24 9B12 0 JRNL AUTH M.A.MICHEL,S.SCUTTS,D.KOMANDER JRNL TITL LINKAGE AND SUBSTRATE SPECIFICITY CONFERRED BY NZF UBIQUITIN JRNL TITL 2 BINDING DOMAINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 44.2 REMARK 3 NUMBER OF REFLECTIONS : 58347 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: DATA WAS SCALED ANISOTROPICALLY. REMARK 4 REMARK 4 9B12 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1000282367. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.96863 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 : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84203 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 94.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.69700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3:1 WITH RESERVOIR SOLUTION CONTAINING REMARK 280 50% PEG 200 AND 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 55.20650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.09550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.20650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.09550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, B, G, H 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, A, I, J 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 C 417 REMARK 465 PRO C 418 REMARK 465 ASP C 508 REMARK 465 GLY C 509 REMARK 465 GLY C 510 REMARK 465 ARG C 511 REMARK 465 GLN C 512 REMARK 465 GLY D 417 REMARK 465 PRO D 418 REMARK 465 ASP D 419 REMARK 465 ASP D 508 REMARK 465 GLY D 509 REMARK 465 GLY D 510 REMARK 465 ARG D 511 REMARK 465 GLN D 512 REMARK 465 GLY E 417 REMARK 465 PHE E 506 REMARK 465 GLU E 507 REMARK 465 ASP E 508 REMARK 465 GLY E 509 REMARK 465 GLY E 510 REMARK 465 ARG E 511 REMARK 465 GLN E 512 REMARK 465 GLY F 417 REMARK 465 PHE F 506 REMARK 465 GLU F 507 REMARK 465 ASP F 508 REMARK 465 GLY F 509 REMARK 465 GLY F 510 REMARK 465 ARG F 511 REMARK 465 GLN F 512 REMARK 465 GLY A 151 REMARK 465 GLY A 152 REMARK 465 GLY B 151 REMARK 465 GLY B 152 REMARK 465 ALA G 350 REMARK 465 ALA H 350 REMARK 465 ALA I 350 REMARK 465 ALA J 350 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS C 424 CG CD CE NZ REMARK 470 GLU C 428 CG CD OE1 OE2 REMARK 470 GLU C 446 CG CD OE1 OE2 REMARK 470 LYS C 448 CG CD CE NZ REMARK 470 LYS C 453 CG CD CE NZ REMARK 470 THR C 460 OG1 CG2 REMARK 470 ARG D 420 CG CD NE CZ NH1 NH2 REMARK 470 LEU D 423 CG CD1 CD2 REMARK 470 LYS D 424 CG CD CE NZ REMARK 470 LEU D 442 CG CD1 CD2 REMARK 470 LYS D 453 CG CD CE NZ REMARK 470 GLU D 456 CG CD OE1 OE2 REMARK 470 LYS D 501 CG CD CE NZ REMARK 470 LYS E 424 CG CD CE NZ REMARK 470 LYS E 453 CD CE NZ REMARK 470 GLN E 491 CG CD OE1 NE2 REMARK 470 ASN E 503 CG OD1 ND2 REMARK 470 ASP E 504 CG OD1 OD2 REMARK 470 LYS F 453 CG CD CE NZ REMARK 470 GLU F 456 CG CD OE1 OE2 REMARK 470 LYS F 484 CE NZ REMARK 470 GLN F 491 CD OE1 NE2 REMARK 470 ASP F 504 CG OD1 OD2 REMARK 470 MET A 1 CG SD CE REMARK 470 PHE A 4 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 THR A 7 OG1 CG2 REMARK 470 THR A 14 OG1 CG2 REMARK 470 LEU A 15 CG CD1 CD2 REMARK 470 GLU A 16 CG CD OE1 OE2 REMARK 470 SER A 20 OG REMARK 470 ASP A 21 CG OD1 OD2 REMARK 470 THR A 22 OG1 CG2 REMARK 470 ILE A 23 CG1 CG2 CD1 REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 ASN A 25 CG OD1 ND2 REMARK 470 VAL A 26 CG1 CG2 REMARK 470 LYS A 27 CG CD CE NZ REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 ILE A 30 CG1 CG2 CD1 REMARK 470 ASP A 32 CG OD1 OD2 REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 GLN A 41 CG CD OE1 NE2 REMARK 470 ARG A 42 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 43 CG CD1 CD2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 ASP A 52 CG OD1 OD2 REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 THR A 55 OG1 CG2 REMARK 470 LEU A 56 CG CD1 CD2 REMARK 470 ASP A 58 CG OD1 OD2 REMARK 470 ASN A 60 CB CG OD1 ND2 REMARK 470 ILE A 61 CG1 CG2 CD1 REMARK 470 GLN A 62 CG CD OE1 NE2 REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 SER A 65 OG REMARK 470 THR A 66 OG1 CG2 REMARK 470 LEU A 69 CD2 REMARK 470 ARG A 150 CG CD NE CZ NH1 NH2 REMARK 470 MET B 1 CG SD CE REMARK 470 GLN B 2 CG CD OE1 NE2 REMARK 470 PHE B 4 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL B 5 CG1 CG2 REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 THR B 7 OG1 CG2 REMARK 470 LEU B 8 CG CD1 CD2 REMARK 470 THR B 9 OG1 CG2 REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 THR B 12 OG1 CG2 REMARK 470 ILE B 13 CG1 CG2 CD1 REMARK 470 THR B 14 OG1 CG2 REMARK 470 LEU B 15 CG CD1 CD2 REMARK 470 GLU B 16 CG CD OE1 OE2 REMARK 470 VAL B 17 CG1 CG2 REMARK 470 SER B 20 OG REMARK 470 ASP B 21 CG OD1 OD2 REMARK 470 THR B 22 OG1 CG2 REMARK 470 ILE B 23 CG1 CG2 CD1 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 ASN B 25 CG OD1 ND2 REMARK 470 VAL B 26 CG1 CG2 REMARK 470 LYS B 27 CG CD CE NZ REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 ILE B 30 CG1 CG2 CD1 REMARK 470 GLN B 31 CG CD OE1 NE2 REMARK 470 ASP B 32 CG OD1 OD2 REMARK 470 LYS B 33 CG CD CE NZ REMARK 470 GLU B 34 CG CD OE1 OE2 REMARK 470 GLN B 41 CG CD OE1 NE2 REMARK 470 LEU B 43 CG CD1 CD2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 GLN B 49 CG CD OE1 NE2 REMARK 470 LEU B 50 CG CD1 CD2 REMARK 470 GLU B 51 CG CD OE1 OE2 REMARK 470 ASP B 52 CG OD1 OD2 REMARK 470 ARG B 54 CG CD NE CZ NH1 NH2 REMARK 470 THR B 55 OG1 CG2 REMARK 470 LEU B 56 CG CD1 CD2 REMARK 470 SER B 57 OG REMARK 470 ASP B 58 CG OD1 OD2 REMARK 470 ASN B 60 CB CG OD1 ND2 REMARK 470 ILE B 61 CG1 CG2 CD1 REMARK 470 GLN B 62 CG CD OE1 NE2 REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 GLU B 64 CG CD OE1 OE2 REMARK 470 SER B 65 OG REMARK 470 THR B 66 OG1 CG2 REMARK 470 LEU B 67 CG CD1 CD2 REMARK 470 LEU B 69 CG CD1 CD2 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 O HOH A 316 O HOH A 318 1.96 REMARK 500 OD2 ASP D 445 O HOH D 601 2.10 REMARK 500 O VAL A 5 OG1 THR A 12 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 NH2 ARG A 148 OE2 GLU G 362 2555 1.98 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 GLU A 16 116.75 -178.46 REMARK 500 PRO A 19 0.16 -55.62 REMARK 500 LEU A 56 1.03 -68.19 REMARK 500 LYS B 11 118.68 -160.31 REMARK 500 THR B 12 119.97 -162.30 REMARK 500 GLU B 16 128.77 179.97 REMARK 500 THR I 360 -0.90 75.95 REMARK 500 GLU I 374 19.48 58.66 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 F 727 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH G 514 DISTANCE = 6.34 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGE C 602 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 ZN G 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS G 356 SG REMARK 620 2 CYS G 359 SG 111.4 REMARK 620 3 CYS G 370 SG 113.7 102.0 REMARK 620 4 CYS G 373 SG 104.9 118.2 106.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS H 356 SG REMARK 620 2 CYS H 359 SG 108.8 REMARK 620 3 CYS H 370 SG 110.3 105.8 REMARK 620 4 CYS H 373 SG 96.7 125.5 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN I 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS I 356 SG REMARK 620 2 CYS I 359 SG 108.1 REMARK 620 3 CYS I 370 SG 110.9 105.6 REMARK 620 4 CYS I 373 SG 105.5 117.9 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN J 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS J 356 SG REMARK 620 2 CYS J 359 SG 110.1 REMARK 620 3 CYS J 370 SG 108.6 105.3 REMARK 620 4 CYS J 373 SG 101.2 124.5 106.3 REMARK 620 N 1 2 3 DBREF 9B12 C 419 512 UNP Q96CV9 OPTN_HUMAN 419 512 DBREF 9B12 D 419 512 UNP Q96CV9 OPTN_HUMAN 419 512 DBREF 9B12 E 419 512 UNP Q96CV9 OPTN_HUMAN 419 512 DBREF 9B12 F 419 512 UNP Q96CV9 OPTN_HUMAN 419 512 DBREF 9B12 A 1 152 UNP P0CG47 UBB_HUMAN 1 152 DBREF 9B12 B 1 152 UNP P0CG47 UBB_HUMAN 1 152 DBREF 9B12 G 350 379 UNP Q96EP0 RNF31_HUMAN 350 379 DBREF 9B12 H 350 379 UNP Q96EP0 RNF31_HUMAN 350 379 DBREF 9B12 I 350 379 UNP Q96EP0 RNF31_HUMAN 350 379 DBREF 9B12 J 350 379 UNP Q96EP0 RNF31_HUMAN 350 379 SEQADV 9B12 GLY C 417 UNP Q96CV9 EXPRESSION TAG SEQADV 9B12 PRO C 418 UNP Q96CV9 EXPRESSION TAG SEQADV 9B12 GLY D 417 UNP Q96CV9 EXPRESSION TAG SEQADV 9B12 PRO D 418 UNP Q96CV9 EXPRESSION TAG SEQADV 9B12 GLY E 417 UNP Q96CV9 EXPRESSION TAG SEQADV 9B12 PRO E 418 UNP Q96CV9 EXPRESSION TAG SEQADV 9B12 GLY F 417 UNP Q96CV9 EXPRESSION TAG SEQADV 9B12 PRO F 418 UNP Q96CV9 EXPRESSION TAG SEQRES 1 C 96 GLY PRO ASP ARG ALA VAL LEU LYS GLU LEU SER GLU LYS SEQRES 2 C 96 LEU GLU LEU ALA GLU LYS ALA LEU ALA SER LYS GLN LEU SEQRES 3 C 96 GLN MET ASP GLU MET LYS GLN THR ILE ALA LYS GLN GLU SEQRES 4 C 96 GLU ASP LEU GLU THR MET THR ILE LEU ARG ALA GLN MET SEQRES 5 C 96 GLU VAL TYR CYS SER ASP PHE HIS ALA GLU ARG ALA ALA SEQRES 6 C 96 ARG GLU LYS ILE HIS GLU GLU LYS GLU GLN LEU ALA LEU SEQRES 7 C 96 GLN LEU ALA VAL LEU LEU LYS GLU ASN ASP ALA PHE GLU SEQRES 8 C 96 ASP GLY GLY ARG GLN SEQRES 1 D 96 GLY PRO ASP ARG ALA VAL LEU LYS GLU LEU SER GLU LYS SEQRES 2 D 96 LEU GLU LEU ALA GLU LYS ALA LEU ALA SER LYS GLN LEU SEQRES 3 D 96 GLN MET ASP GLU MET LYS GLN THR ILE ALA LYS GLN GLU SEQRES 4 D 96 GLU ASP LEU GLU THR MET THR ILE LEU ARG ALA GLN MET SEQRES 5 D 96 GLU VAL TYR CYS SER ASP PHE HIS ALA GLU ARG ALA ALA SEQRES 6 D 96 ARG GLU LYS ILE HIS GLU GLU LYS GLU GLN LEU ALA LEU SEQRES 7 D 96 GLN LEU ALA VAL LEU LEU LYS GLU ASN ASP ALA PHE GLU SEQRES 8 D 96 ASP GLY GLY ARG GLN SEQRES 1 E 96 GLY PRO ASP ARG ALA VAL LEU LYS GLU LEU SER GLU LYS SEQRES 2 E 96 LEU GLU LEU ALA GLU LYS ALA LEU ALA SER LYS GLN LEU SEQRES 3 E 96 GLN MET ASP GLU MET LYS GLN THR ILE ALA LYS GLN GLU SEQRES 4 E 96 GLU ASP LEU GLU THR MET THR ILE LEU ARG ALA GLN MET SEQRES 5 E 96 GLU VAL TYR CYS SER ASP PHE HIS ALA GLU ARG ALA ALA SEQRES 6 E 96 ARG GLU LYS ILE HIS GLU GLU LYS GLU GLN LEU ALA LEU SEQRES 7 E 96 GLN LEU ALA VAL LEU LEU LYS GLU ASN ASP ALA PHE GLU SEQRES 8 E 96 ASP GLY GLY ARG GLN SEQRES 1 F 96 GLY PRO ASP ARG ALA VAL LEU LYS GLU LEU SER GLU LYS SEQRES 2 F 96 LEU GLU LEU ALA GLU LYS ALA LEU ALA SER LYS GLN LEU SEQRES 3 F 96 GLN MET ASP GLU MET LYS GLN THR ILE ALA LYS GLN GLU SEQRES 4 F 96 GLU ASP LEU GLU THR MET THR ILE LEU ARG ALA GLN MET SEQRES 5 F 96 GLU VAL TYR CYS SER ASP PHE HIS ALA GLU ARG ALA ALA SEQRES 6 F 96 ARG GLU LYS ILE HIS GLU GLU LYS GLU GLN LEU ALA LEU SEQRES 7 F 96 GLN LEU ALA VAL LEU LEU LYS GLU ASN ASP ALA PHE GLU SEQRES 8 F 96 ASP GLY GLY ARG GLN SEQRES 1 A 152 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 152 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 152 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 152 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 152 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 152 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY MET GLN SEQRES 7 A 152 ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE THR LEU SEQRES 8 A 152 GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL LYS ALA SEQRES 9 A 152 LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN GLN SEQRES 10 A 152 ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP GLY ARG SEQRES 11 A 152 THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER THR LEU SEQRES 12 A 152 HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 152 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 152 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 152 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 152 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 152 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 152 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY MET GLN SEQRES 7 B 152 ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE THR LEU SEQRES 8 B 152 GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL LYS ALA SEQRES 9 B 152 LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN GLN SEQRES 10 B 152 ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP GLY ARG SEQRES 11 B 152 THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER THR LEU SEQRES 12 B 152 HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 G 30 ALA ARG GLY ARG TRP ALA CYS GLN SER CYS THR PHE GLU SEQRES 2 G 30 ASN GLU ALA ALA ALA VAL LEU CYS SER ILE CYS GLU ARG SEQRES 3 G 30 PRO ARG LEU ALA SEQRES 1 H 30 ALA ARG GLY ARG TRP ALA CYS GLN SER CYS THR PHE GLU SEQRES 2 H 30 ASN GLU ALA ALA ALA VAL LEU CYS SER ILE CYS GLU ARG SEQRES 3 H 30 PRO ARG LEU ALA SEQRES 1 I 30 ALA ARG GLY ARG TRP ALA CYS GLN SER CYS THR PHE GLU SEQRES 2 I 30 ASN GLU ALA ALA ALA VAL LEU CYS SER ILE CYS GLU ARG SEQRES 3 I 30 PRO ARG LEU ALA SEQRES 1 J 30 ALA ARG GLY ARG TRP ALA CYS GLN SER CYS THR PHE GLU SEQRES 2 J 30 ASN GLU ALA ALA ALA VAL LEU CYS SER ILE CYS GLU ARG SEQRES 3 J 30 PRO ARG LEU ALA HET PG4 C 601 13 HET PGE C 602 8 HET CL F 601 1 HET EPE F 602 15 HET EPE A 201 32 HET CL B 201 1 HET ZN G 401 1 HET ZN H 401 1 HET EPE H 402 15 HET ZN I 401 1 HET ZN J 401 1 HET PG4 J 402 13 HET CL J 403 1 HET EPE J 404 15 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM CL CHLORIDE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM ZN ZINC ION HETSYN EPE HEPES FORMUL 11 PG4 2(C8 H18 O5) FORMUL 12 PGE C6 H14 O4 FORMUL 13 CL 3(CL 1-) FORMUL 14 EPE 4(C8 H18 N2 O4 S) FORMUL 17 ZN 4(ZN 2+) FORMUL 25 HOH *187(H2 O) HELIX 1 AA1 ASP C 419 ALA C 505 1 87 HELIX 2 AA2 ALA D 421 GLU D 507 1 87 HELIX 3 AA3 ASP E 419 GLU E 459 1 41 HELIX 4 AA4 GLU E 459 ALA E 505 1 47 HELIX 5 AA5 ASP F 419 ALA F 505 1 87 HELIX 6 AA6 THR A 22 GLY A 35 1 14 HELIX 7 AA7 PRO A 37 ASP A 39 5 3 HELIX 8 AA8 THR A 98 GLY A 111 1 14 HELIX 9 AA9 PRO A 113 ASP A 115 5 3 HELIX 10 AB1 THR A 131 ASN A 136 1 6 HELIX 11 AB2 THR B 22 ILE B 30 1 9 HELIX 12 AB3 ILE B 30 GLY B 35 1 6 HELIX 13 AB4 PRO B 37 ASP B 39 5 3 HELIX 14 AB5 THR B 98 GLY B 111 1 14 HELIX 15 AB6 PRO B 113 ASP B 115 5 3 SHEET 1 AA1 3 PHE A 4 THR A 7 0 SHEET 2 AA1 3 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 3 AA1 3 GLN A 41 ILE A 44 -1 N ARG A 42 O VAL A 70 SHEET 1 AA2 5 THR A 88 GLU A 92 0 SHEET 2 AA2 5 GLN A 78 THR A 83 -1 N ILE A 79 O LEU A 91 SHEET 3 AA2 5 THR A 142 LEU A 147 1 O LEU A 143 N PHE A 80 SHEET 4 AA2 5 GLN A 117 PHE A 121 -1 N ARG A 118 O VAL A 146 SHEET 5 AA2 5 LYS A 124 GLN A 125 -1 O LYS A 124 N PHE A 121 SHEET 1 AA3 3 PHE B 4 LYS B 6 0 SHEET 2 AA3 3 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 3 AA3 3 GLN B 41 LEU B 43 -1 N ARG B 42 O VAL B 70 SHEET 1 AA4 5 THR B 88 GLU B 92 0 SHEET 2 AA4 5 GLN B 78 THR B 83 -1 N ILE B 79 O LEU B 91 SHEET 3 AA4 5 THR B 142 LEU B 147 1 O LEU B 145 N LYS B 82 SHEET 4 AA4 5 GLN B 117 PHE B 121 -1 N ARG B 118 O VAL B 146 SHEET 5 AA4 5 LYS B 124 GLN B 125 -1 O LYS B 124 N PHE B 121 SHEET 1 AA5 2 TRP G 354 ALA G 355 0 SHEET 2 AA5 2 GLU G 362 ASN G 363 -1 O ASN G 363 N TRP G 354 SHEET 1 AA6 2 TRP H 354 ALA H 355 0 SHEET 2 AA6 2 GLU H 362 ASN H 363 -1 O ASN H 363 N TRP H 354 SHEET 1 AA7 2 TRP I 354 ALA I 355 0 SHEET 2 AA7 2 GLU I 362 ASN I 363 -1 O ASN I 363 N TRP I 354 SHEET 1 AA8 2 TRP J 354 ALA J 355 0 SHEET 2 AA8 2 GLU J 362 ASN J 363 -1 O ASN J 363 N TRP J 354 LINK SG CYS G 356 ZN ZN G 401 1555 1555 2.30 LINK SG CYS G 359 ZN ZN G 401 1555 1555 2.28 LINK SG CYS G 370 ZN ZN G 401 1555 1555 2.30 LINK SG CYS G 373 ZN ZN G 401 1555 1555 2.34 LINK SG CYS H 356 ZN ZN H 401 1555 1555 2.34 LINK SG CYS H 359 ZN ZN H 401 1555 1555 2.35 LINK SG CYS H 370 ZN ZN H 401 1555 1555 2.26 LINK SG CYS H 373 ZN ZN H 401 1555 1555 2.30 LINK SG CYS I 356 ZN ZN I 401 1555 1555 2.30 LINK SG CYS I 359 ZN ZN I 401 1555 1555 2.28 LINK SG CYS I 370 ZN ZN I 401 1555 1555 2.31 LINK SG CYS I 373 ZN ZN I 401 1555 1555 2.29 LINK SG CYS J 356 ZN ZN J 401 1555 1555 2.33 LINK SG CYS J 359 ZN ZN J 401 1555 1555 2.31 LINK SG CYS J 370 ZN ZN J 401 1555 1555 2.32 LINK SG CYS J 373 ZN ZN J 401 1555 1555 2.33 CRYST1 110.413 70.191 193.944 90.00 102.25 90.00 C 1 2 1 16 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 0.009057 0.000000 0.001966 0.00000 SCALE2 0.000000 0.014247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005276 0.00000