HEADER LIGASE 10-MAR-25 9M7O TITLE CRYO-EM STRUCTURE OF UFD2/UBC4-UB COMPLEX WITH K29TRIUB(MONOMERIC TITLE 2 CONFORMATION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 4; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME 4,UBIQUITIN CARRIER PROTEIN COMPND 5 4,UBIQUITIN-PROTEIN LIGASE 4; COMPND 6 EC: 2.3.2.23; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: POLYUBIQUITIN-C; COMPND 11 CHAIN: D; COMPND 12 SYNONYM: PROXIMAL UB OF K29TIRUB; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: POLYUBIQUITIN-C; COMPND 17 CHAIN: E; COMPND 18 SYNONYM: DISTAL UB OF K29TIRUB; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES; COMPND 21 MOL_ID: 4; COMPND 22 MOLECULE: UBIQUITIN; COMPND 23 CHAIN: C; COMPND 24 SYNONYM: DONOR UB; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 5; COMPND 27 MOLECULE: E4 UBIQUITIN-PROTEIN LIGASE UFD2; COMPND 28 CHAIN: A; COMPND 29 SYNONYM: RING-TYPE E3 UBIQUITIN TRANSFERASE UFD2,UBIQUITIN COMPND 30 CONJUGATION FACTOR E4,UBIQUITIN FUSION DEGRADATION PROTEIN 2,UB COMPND 31 FUSION PROTEIN 2; COMPND 32 EC: 2.3.2.27; COMPND 33 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BREWER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 GENE: UBC4, YBR082C, YBR0745; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: UBC; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 GENE: UBC; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 23 MOL_ID: 4; SOURCE 24 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 25 ORGANISM_COMMON: HUMAN; SOURCE 26 ORGANISM_TAXID: 9606; SOURCE 27 GENE: RPS27A, UBA80, UBCEP1; SOURCE 28 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 29 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 30 MOL_ID: 5; SOURCE 31 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 32 S288C); SOURCE 33 ORGANISM_COMMON: BREWER'S YEAST; SOURCE 34 ORGANISM_TAXID: 559292; SOURCE 35 GENE: UFD2, YDL190C, D1255; SOURCE 36 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 37 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E4 ENZYME, UFD2, BRANCH UB CHAINS, LIGASE EXPDTA ELECTRON MICROSCOPY AUTHOR Z.B.TONG,L.LIU REVDAT 3 18-FEB-26 9M7O 1 JRNL REVDAT 2 27-AUG-25 9M7O 1 JRNL REVDAT 1 30-JUL-25 9M7O 0 JRNL AUTH Z.TONG,X.WU,H.CAI,S.WU,T.ZHANG,Z.DENG,Z.XU,R.YUAN,H.AI, JRNL AUTH 2 L.LIU,M.PAN JRNL TITL STRUCTURAL BASIS FOR E4 ENZYME UFD2-CATALYZED K48/K29 JRNL TITL 2 BRANCHED UBIQUITIN CHAINS. JRNL REF NAT.CHEM.BIOL. V. 22 239 2026 JRNL REFN ESSN 1552-4469 JRNL PMID 40817136 JRNL DOI 10.1038/S41589-025-01985-2 REMARK 2 REMARK 2 RESOLUTION. 4.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.140 REMARK 3 NUMBER OF PARTICLES : 347924 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9M7O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 14-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057356. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CRYO-EM STRUCTURE OF UFD2/UBC4 REMARK 245 -UB COMPLEX WITH REMARK 245 K29TRIUB(MONOMERIC CONFORMATION) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, E, C, 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 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 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 ILE A 4 REMARK 465 GLU A 5 REMARK 465 ASP A 6 REMARK 465 ILE A 7 REMARK 465 LEU A 8 REMARK 465 GLN A 9 REMARK 465 ILE A 10 REMARK 465 THR A 11 REMARK 465 THR A 12 REMARK 465 ASP A 13 REMARK 465 PRO A 14 REMARK 465 SER A 15 REMARK 465 ASP A 16 REMARK 465 THR A 17 REMARK 465 ARG A 18 REMARK 465 GLY A 19 REMARK 465 TYR A 20 REMARK 465 SER A 21 REMARK 465 LEU A 22 REMARK 465 LEU A 23 REMARK 465 LYS A 24 REMARK 465 SER A 25 REMARK 465 GLU A 26 REMARK 465 GLU A 27 REMARK 465 VAL A 28 REMARK 465 PRO A 29 REMARK 465 GLN A 30 REMARK 465 GLY A 31 REMARK 465 SER A 32 REMARK 465 THR A 33 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 VAL A 36 REMARK 465 ASP A 37 REMARK 465 PHE A 38 REMARK 465 ILE A 39 REMARK 465 ASP A 40 REMARK 465 THR A 41 REMARK 465 LEU A 42 REMARK 465 LEU A 43 REMARK 465 LEU A 44 REMARK 465 TYR A 45 REMARK 465 GLN A 46 REMARK 465 LEU A 47 REMARK 465 THR A 48 REMARK 465 GLU A 49 REMARK 465 ASN A 50 REMARK 465 GLU A 51 REMARK 465 LYS A 52 REMARK 465 LEU A 53 REMARK 465 ASP A 54 REMARK 465 LYS A 55 REMARK 465 PRO A 56 REMARK 465 PHE A 57 REMARK 465 GLU A 58 REMARK 465 TYR A 59 REMARK 465 LEU A 60 REMARK 465 ASN A 61 REMARK 465 ASP A 62 REMARK 465 CYS A 63 REMARK 465 PHE A 64 REMARK 465 ARG A 65 REMARK 465 ARG A 66 REMARK 465 ASN A 67 REMARK 465 GLN A 68 REMARK 465 GLN A 69 REMARK 465 GLN A 70 REMARK 465 LYS A 71 REMARK 465 ARG A 72 REMARK 465 ILE A 73 REMARK 465 THR A 74 REMARK 465 LYS A 75 REMARK 465 ASN A 76 REMARK 465 LYS A 77 REMARK 465 PRO A 78 REMARK 465 ASN A 79 REMARK 465 ALA A 80 REMARK 465 GLU A 81 REMARK 465 SER A 82 REMARK 465 LEU A 83 REMARK 465 HIS A 84 REMARK 465 SER A 85 REMARK 465 THR A 86 REMARK 465 PHE A 87 REMARK 465 GLN A 88 REMARK 465 GLU A 89 REMARK 465 ILE A 90 REMARK 465 ASP A 91 REMARK 465 ARG A 92 REMARK 465 LEU A 93 REMARK 465 VAL A 94 REMARK 465 ILE A 95 REMARK 465 GLY A 96 REMARK 465 TYR A 97 REMARK 465 GLY A 98 REMARK 465 VAL A 99 REMARK 465 VAL A 100 REMARK 465 ALA A 101 REMARK 465 LEU A 102 REMARK 465 GLN A 103 REMARK 465 ILE A 104 REMARK 465 GLU A 105 REMARK 465 ASN A 106 REMARK 465 PHE A 107 REMARK 465 CYS A 108 REMARK 465 MET A 109 REMARK 465 ASN A 110 REMARK 465 GLY A 111 REMARK 465 ALA A 112 REMARK 465 PHE A 113 REMARK 465 ILE A 114 REMARK 465 ASN A 115 REMARK 465 TYR A 116 REMARK 465 LYS A 373 REMARK 465 THR A 374 REMARK 465 ALA A 375 REMARK 465 ASP A 376 REMARK 465 PRO A 498 REMARK 465 LEU A 499 REMARK 465 ILE A 500 REMARK 465 PRO A 501 REMARK 465 ASP A 502 REMARK 465 GLN A 503 REMARK 465 ILE A 504 REMARK 465 GLY A 505 REMARK 465 VAL A 506 REMARK 465 GLU A 507 REMARK 465 ASN A 508 REMARK 465 VAL A 509 REMARK 465 ASP A 510 REMARK 465 ASN A 511 REMARK 465 ALA A 512 REMARK 465 ASP A 513 REMARK 465 THR A 628 REMARK 465 GLY A 629 REMARK 465 SER A 630 REMARK 465 SER A 631 REMARK 465 SER A 632 REMARK 465 ARG A 708 REMARK 465 ALA A 709 REMARK 465 ARG A 710 REMARK 465 GLY A 711 REMARK 465 ALA A 712 REMARK 465 PRO A 713 REMARK 465 PRO A 714 REMARK 465 THR A 715 REMARK 465 ARG A 716 REMARK 465 GLU A 717 REMARK 465 GLU A 718 REMARK 465 GLU A 719 REMARK 465 LYS A 956 REMARK 465 HIS A 957 REMARK 465 LYS A 958 REMARK 465 ALA A 959 REMARK 465 SER A 960 REMARK 465 GLU A 961 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 ARG E 29 CG CD NE CZ NH1 NH2 REMARK 470 ARG E 74 CG CD NE CZ NH1 NH2 REMARK 470 MET C 1 CG SD CE REMARK 470 GLN C 2 CG CD OE1 NE2 REMARK 470 ILE C 3 CG1 CG2 CD1 REMARK 470 LEU C 15 CG CD1 CD2 REMARK 470 VAL C 17 CG1 CG2 REMARK 470 SER C 20 OG REMARK 470 ILE C 30 CG1 CG2 CD1 REMARK 470 GLU C 34 CG CD OE1 OE2 REMARK 470 ILE C 36 CG1 CG2 CD1 REMARK 470 ASP C 39 CG OD1 OD2 REMARK 470 GLN C 40 CG CD OE1 NE2 REMARK 470 GLN C 41 CG CD OE1 NE2 REMARK 470 TYR C 59 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS C 63 CG CD CE NZ REMARK 470 LEU C 67 CG CD1 CD2 REMARK 470 LEU C 71 CG CD1 CD2 REMARK 470 LEU C 73 CG CD1 CD2 REMARK 470 ARG C 74 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 175 CG OD1 ND2 REMARK 470 ARG A 241 CG CD NE CZ NH1 NH2 REMARK 470 MET A 248 CG SD CE REMARK 470 LYS A 258 CG CD CE NZ REMARK 470 ARG A 296 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 309 CG OD1 ND2 REMARK 470 ASN A 314 CG OD1 ND2 REMARK 470 HIS A 428 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 452 CG CD1 CD2 REMARK 470 VAL A 521 CG1 CG2 REMARK 470 GLU A 528 CG CD OE1 OE2 REMARK 470 GLU A 626 CG CD OE1 OE2 REMARK 470 GLN A 633 CG CD OE1 NE2 REMARK 470 PHE A 634 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 635 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 637 CG CD CE NZ REMARK 470 ARG A 641 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 674 CG1 CG2 REMARK 470 LEU A 834 CG CD1 CD2 REMARK 470 SER A 850 OG REMARK 470 MET A 927 CG SD CE 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 OH TYR A 174 OE2 GLU A 256 2.13 REMARK 500 OE1 GLU A 404 OH TYR A 540 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 597 CB PRO A 597 CG -0.354 REMARK 500 PRO A 597 CG PRO A 597 CD -0.348 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 597 CA - N - CD ANGL. DEV. = -10.1 DEGREES REMARK 500 PRO A 597 CA - CB - CG ANGL. DEV. = -37.0 DEGREES REMARK 500 PRO A 597 CB - CG - CD ANGL. DEV. = 31.6 DEGREES REMARK 500 PRO A 597 N - CD - CG ANGL. DEV. = -29.4 DEGREES 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 B 60 54.09 -118.81 REMARK 500 ASN C 60 41.52 37.98 REMARK 500 ASN A 340 32.16 -99.10 REMARK 500 ASN A 371 19.30 59.16 REMARK 500 ILE A 663 -51.31 80.36 REMARK 500 ASP A 791 72.62 52.30 REMARK 500 SER A 920 53.78 -92.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62355 RELATED DB: EMDB DBREF 9M7O B 1 148 UNP P15731 UBC4_YEAST 1 148 DBREF 9M7O D 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 9M7O E 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 9M7O C 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 9M7O A 1 961 UNP P54860 UFD2_YEAST 1 961 SEQADV 9M7O SER B 22 UNP P15731 CYS 22 ENGINEERED MUTATION SEQADV 9M7O SER B 108 UNP P15731 CYS 108 ENGINEERED MUTATION SEQADV 9M7O CYS D 48 UNP P0CG48 LYS 48 ENGINEERED MUTATION SEQADV 9M7O ASP D 77 UNP P0CG48 EXPRESSION TAG SEQADV 9M7O ARG E 29 UNP P0CG48 LYS 29 ENGINEERED MUTATION SEQRES 1 B 148 MET SER SER SER LYS ARG ILE ALA LYS GLU LEU SER ASP SEQRES 2 B 148 LEU GLU ARG ASP PRO PRO THR SER SER SER ALA GLY PRO SEQRES 3 B 148 VAL GLY ASP ASP LEU TYR HIS TRP GLN ALA SER ILE MET SEQRES 4 B 148 GLY PRO ALA ASP SER PRO TYR ALA GLY GLY VAL PHE PHE SEQRES 5 B 148 LEU SER ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO SEQRES 6 B 148 PRO LYS ILE SER PHE THR THR LYS ILE TYR HIS PRO ASN SEQRES 7 B 148 ILE ASN ALA ASN GLY ASN ILE CYS LEU ASP ILE LEU LYS SEQRES 8 B 148 ASP GLN TRP SER PRO ALA LEU THR LEU SER LYS VAL LEU SEQRES 9 B 148 LEU SER ILE SER SER LEU LEU THR ASP ALA ASN PRO ASP SEQRES 10 B 148 ASP PRO LEU VAL PRO GLU ILE ALA HIS ILE TYR LYS THR SEQRES 11 B 148 ASP ARG PRO LYS TYR GLU ALA THR ALA ARG GLU TRP THR SEQRES 12 B 148 LYS LYS TYR ALA VAL SEQRES 1 D 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 77 GLN GLN ARG LEU ILE PHE ALA GLY CYS GLN LEU GLU ASP SEQRES 5 D 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 76 LYS ALA ARG ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 A 961 MET THR ALA ILE GLU ASP ILE LEU GLN ILE THR THR ASP SEQRES 2 A 961 PRO SER ASP THR ARG GLY TYR SER LEU LEU LYS SER GLU SEQRES 3 A 961 GLU VAL PRO GLN GLY SER THR LEU GLY VAL ASP PHE ILE SEQRES 4 A 961 ASP THR LEU LEU LEU TYR GLN LEU THR GLU ASN GLU LYS SEQRES 5 A 961 LEU ASP LYS PRO PHE GLU TYR LEU ASN ASP CYS PHE ARG SEQRES 6 A 961 ARG ASN GLN GLN GLN LYS ARG ILE THR LYS ASN LYS PRO SEQRES 7 A 961 ASN ALA GLU SER LEU HIS SER THR PHE GLN GLU ILE ASP SEQRES 8 A 961 ARG LEU VAL ILE GLY TYR GLY VAL VAL ALA LEU GLN ILE SEQRES 9 A 961 GLU ASN PHE CYS MET ASN GLY ALA PHE ILE ASN TYR ILE SEQRES 10 A 961 THR GLY ILE VAL SER ASN VAL ASN SER TYR THR ASP PHE SEQRES 11 A 961 LEU SER GLN ILE ILE GLN ARG ALA ILE LEU GLU GLY THR SEQRES 12 A 961 ALA LEU ASP LEU LEU ASN ALA VAL PHE PRO THR LEU LEU SEQRES 13 A 961 GLU TYR CYS ASN LYS HIS VAL SER HIS PHE ASP LEU ASN SEQRES 14 A 961 GLU SER VAL ILE TYR ASN ASN VAL LEU THR ILE PHE GLU SEQRES 15 A 961 LEU PHE VAL THR PHE LYS PRO ILE ALA GLU ILE PHE THR SEQRES 16 A 961 LYS ILE ASP GLY PHE PHE ALA ASP TYR SER CYS LYS PRO SEQRES 17 A 961 GLN ASP PHE GLU ARG LYS THR ILE LEU GLY PRO ILE LEU SEQRES 18 A 961 SER LEU SER PRO ILE GLU ALA ALA VAL ALA ILE ARG ASN SEQRES 19 A 961 TYR GLY ASP ASN LEU LEU ARG SER LYS GLN GLN THR ALA SEQRES 20 A 961 MET ILE HIS GLU SER LEU GLN ALA GLU HIS LYS VAL VAL SEQRES 21 A 961 ILE ASP ARG LEU PHE PHE ILE VAL ASP LYS LEU VAL ARG SEQRES 22 A 961 GLY SER LEU ASN SER ARG THR ASP MET ILE SER TYR PHE SEQRES 23 A 961 ALA HIS ILE ALA ASN LYS ASN HIS LEU ARG ARG ALA ASP SEQRES 24 A 961 HIS PRO PRO PHE LYS GLU LEU SER SER ASN GLY PHE MET SEQRES 25 A 961 SER ASN ILE THR LEU LEU LEU VAL ARG PHE SER GLN PRO SEQRES 26 A 961 PHE LEU ASP ILE SER TYR LYS LYS ILE ASP LYS ILE ASP SEQRES 27 A 961 ALA ASN TYR PHE ASN ASN PRO SER LEU PHE ILE ASP LEU SEQRES 28 A 961 SER GLY GLU THR ARG LEU ASN SER ASP PHE LYS GLU ALA SEQRES 29 A 961 ASP ALA PHE TYR ASP LYS ASN ARG LYS THR ALA ASP SER SEQRES 30 A 961 LYS PRO ASN PHE ILE SER ASP CYS PHE PHE LEU THR LEU SEQRES 31 A 961 THR TYR LEU HIS TYR GLY LEU GLY GLY THR LEU SER PHE SEQRES 32 A 961 GLU GLU LYS MET GLY SER GLU ILE LYS ALA LEU LYS GLU SEQRES 33 A 961 GLU ILE GLU LYS VAL LYS LYS ILE ALA ALA ASN HIS ASP SEQRES 34 A 961 VAL PHE ALA ARG PHE ILE THR ALA GLN LEU SER LYS MET SEQRES 35 A 961 GLU LYS ALA LEU LYS THR THR GLU SER LEU ARG PHE ALA SEQRES 36 A 961 LEU GLN GLY PHE PHE ALA HIS ARG SER LEU GLN LEU GLU SEQRES 37 A 961 VAL PHE ASP PHE ILE CYS GLY ALA SER THR PHE LEU ILE SEQRES 38 A 961 ARG VAL VAL ASP PRO GLU HIS GLU PHE PRO PHE LYS GLN SEQRES 39 A 961 ILE LYS LEU PRO LEU ILE PRO ASP GLN ILE GLY VAL GLU SEQRES 40 A 961 ASN VAL ASP ASN ALA ASP PHE LEU ARG ALA HIS ALA PRO SEQRES 41 A 961 VAL PRO PHE LYS TYR TYR PRO GLU PHE VAL VAL GLU GLY SEQRES 42 A 961 PRO VAL ASN TYR SER LEU TYR ILE SER LYS TYR GLN THR SEQRES 43 A 961 SER PRO ILE PHE ARG ASN PRO ARG LEU GLY SER PHE VAL SEQRES 44 A 961 GLU PHE THR THR MET VAL LEU ARG CYS PRO GLU LEU VAL SEQRES 45 A 961 SER ASN PRO HIS LEU LYS GLY LYS LEU VAL GLN LEU LEU SEQRES 46 A 961 SER VAL GLY ALA MET PRO LEU THR ASP ASN SER PRO GLY SEQRES 47 A 961 PHE MET MET ASP ILE PHE GLU HIS ASP GLU LEU VAL ASN SEQRES 48 A 961 LYS ASN LEU LEU TYR ALA LEU LEU ASP PHE TYR VAL ILE SEQRES 49 A 961 VAL GLU LYS THR GLY SER SER SER GLN PHE TYR ASP LYS SEQRES 50 A 961 PHE ASN SER ARG TYR SER ILE SER ILE ILE LEU GLU GLU SEQRES 51 A 961 LEU TYR TYR LYS ILE PRO SER TYR LYS ASN GLN LEU ILE SEQRES 52 A 961 TRP GLN SER GLN ASN ASN ALA ASP PHE PHE VAL ARG PHE SEQRES 53 A 961 VAL ALA ARG MET LEU ASN ASP LEU THR PHE LEU LEU ASP SEQRES 54 A 961 GLU GLY LEU SER ASN LEU ALA GLU VAL HIS ASN ILE GLN SEQRES 55 A 961 ASN GLU LEU ASP ASN ARG ALA ARG GLY ALA PRO PRO THR SEQRES 56 A 961 ARG GLU GLU GLU ASP LYS GLU LEU GLN THR ARG LEU ALA SEQRES 57 A 961 SER ALA SER ARG GLN ALA LYS SER SER CYS GLY LEU ALA SEQRES 58 A 961 ASP LYS SER MET LYS LEU PHE GLU ILE TYR SER LYS ASP SEQRES 59 A 961 ILE PRO ALA ALA PHE VAL THR PRO GLU ILE VAL TYR ARG SEQRES 60 A 961 LEU ALA SER MET LEU ASN TYR ASN LEU GLU SER LEU VAL SEQRES 61 A 961 GLY PRO LYS CYS GLY GLU LEU LYS VAL LYS ASP PRO GLN SEQRES 62 A 961 SER TYR SER PHE ASN PRO LYS ASP LEU LEU LYS ALA LEU SEQRES 63 A 961 THR THR VAL TYR ILE ASN LEU SER GLU GLN SER GLU PHE SEQRES 64 A 961 ILE SER ALA VAL ALA LYS ASP GLU ARG SER PHE ASN ARG SEQRES 65 A 961 ASN LEU PHE VAL ARG ALA VAL ASP ILE LEU GLY ARG LYS SEQRES 66 A 961 THR GLY LEU ALA SER PRO GLU PHE ILE GLU LYS LEU LEU SEQRES 67 A 961 ASN PHE ALA ASN LYS ALA GLU GLU GLN ARG LYS ALA ASP SEQRES 68 A 961 GLU GLU GLU ASP LEU GLU TYR GLY ASP VAL PRO ASP GLU SEQRES 69 A 961 PHE LEU ASP PRO LEU MET TYR THR ILE MET LYS ASP PRO SEQRES 70 A 961 VAL ILE LEU PRO ALA SER LYS MET ASN ILE ASP ARG SER SEQRES 71 A 961 THR ILE LYS ALA HIS LEU LEU SER ASP SER THR ASP PRO SEQRES 72 A 961 PHE ASN ARG MET PRO LEU LYS LEU GLU ASP VAL THR PRO SEQRES 73 A 961 ASN GLU GLU LEU ARG GLN LYS ILE LEU CYS PHE LYS LYS SEQRES 74 A 961 GLN LYS LYS GLU GLU ALA LYS HIS LYS ALA SER GLU HELIX 1 AA1 SER B 3 ASP B 17 1 15 HELIX 2 AA2 ASP B 60 LYS B 64 5 5 HELIX 3 AA3 THR B 99 ALA B 114 1 16 HELIX 4 AA4 VAL B 121 LYS B 129 1 9 HELIX 5 AA5 ASP B 131 TYR B 146 1 16 HELIX 6 AA6 THR D 22 GLY D 35 1 14 HELIX 7 AA7 THR E 22 GLY E 35 1 14 HELIX 8 AA8 THR C 22 LYS C 29 1 8 HELIX 9 AA9 PRO C 37 GLN C 41 5 5 HELIX 10 AB1 THR C 55 TYR C 59 5 5 HELIX 11 AB2 THR A 118 ASN A 123 1 6 HELIX 12 AB3 ASN A 123 GLY A 142 1 20 HELIX 13 AB4 THR A 143 LYS A 161 1 19 HELIX 14 AB5 GLU A 170 THR A 186 1 17 HELIX 15 AB6 PHE A 187 GLU A 192 1 6 HELIX 16 AB7 ILE A 193 ILE A 197 5 5 HELIX 17 AB8 LYS A 207 PHE A 211 5 5 HELIX 18 AB9 LEU A 217 SER A 222 1 6 HELIX 19 AC1 GLU A 227 GLY A 236 1 10 HELIX 20 AC2 SER A 242 ARG A 273 1 32 HELIX 21 AC3 SER A 275 ASN A 293 1 19 HELIX 22 AC4 HIS A 294 ALA A 298 5 5 HELIX 23 AC5 SER A 308 SER A 323 1 16 HELIX 24 AC6 GLN A 324 ASP A 328 5 5 HELIX 25 AC7 TYR A 331 ILE A 337 5 7 HELIX 26 AC8 ASP A 360 LYS A 370 1 11 HELIX 27 AC9 ASN A 380 GLY A 396 1 17 HELIX 28 AD1 GLY A 396 LYS A 406 1 11 HELIX 29 AD2 LYS A 406 LYS A 422 1 17 HELIX 30 AD3 HIS A 428 ALA A 461 1 34 HELIX 31 AD4 HIS A 462 ASP A 485 1 24 HELIX 32 AD5 PRO A 520 TYR A 525 1 6 HELIX 33 AD6 GLU A 528 SER A 542 1 15 HELIX 34 AD7 ASN A 552 ARG A 554 5 3 HELIX 35 AD8 LEU A 555 CYS A 568 1 14 HELIX 36 AD9 ASN A 574 ALA A 589 1 16 HELIX 37 AE1 MET A 600 HIS A 606 1 7 HELIX 38 AE2 LEU A 609 VAL A 625 1 17 HELIX 39 AE3 ASP A 636 ILE A 655 1 20 HELIX 40 AE4 ILE A 655 ASN A 669 1 15 HELIX 41 AE5 ASN A 669 ASP A 706 1 38 HELIX 42 AE6 LYS A 721 ILE A 755 1 35 HELIX 43 AE7 PRO A 756 PHE A 759 5 4 HELIX 44 AE8 ILE A 764 GLY A 781 1 18 HELIX 45 AE9 GLY A 781 LEU A 787 1 7 HELIX 46 AF1 ASN A 798 LEU A 813 1 16 HELIX 47 AF2 GLN A 816 LYS A 825 1 10 HELIX 48 AF3 ASN A 831 LYS A 845 1 15 HELIX 49 AF4 SER A 850 GLU A 877 1 28 HELIX 50 AF5 PRO A 882 LEU A 886 5 5 HELIX 51 AF6 ARG A 909 LEU A 917 1 9 HELIX 52 AF7 LYS A 930 VAL A 934 5 5 HELIX 53 AF8 ASN A 937 GLU A 953 1 17 SHEET 1 AA1 4 SER B 22 VAL B 27 0 SHEET 2 AA1 4 ASP B 30 MET B 39 -1 O SER B 37 N SER B 23 SHEET 3 AA1 4 VAL B 50 HIS B 56 -1 O LEU B 53 N ALA B 36 SHEET 4 AA1 4 LYS B 67 PHE B 70 -1 O SER B 69 N SER B 54 SHEET 1 AA2 5 THR D 12 GLU D 16 0 SHEET 2 AA2 5 GLN D 2 THR D 7 -1 N ILE D 3 O LEU D 15 SHEET 3 AA2 5 THR D 66 LEU D 71 1 O LEU D 67 N PHE D 4 SHEET 4 AA2 5 GLN D 41 PHE D 45 -1 N ARG D 42 O VAL D 70 SHEET 5 AA2 5 CYS D 48 GLN D 49 -1 O CYS D 48 N PHE D 45 SHEET 1 AA3 5 THR E 12 GLU E 16 0 SHEET 2 AA3 5 GLN E 2 THR E 7 -1 N VAL E 5 O ILE E 13 SHEET 3 AA3 5 THR E 66 LEU E 69 1 O LEU E 67 N LYS E 6 SHEET 4 AA3 5 LEU E 43 PHE E 45 -1 N ILE E 44 O HIS E 68 SHEET 5 AA3 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45 SHEET 1 AA4 3 THR C 12 LEU C 15 0 SHEET 2 AA4 3 ILE C 3 LYS C 6 -1 N VAL C 5 O ILE C 13 SHEET 3 AA4 3 THR C 66 HIS C 68 1 O LEU C 67 N LYS C 6 SHEET 1 AA5 2 ILE C 44 PHE C 45 0 SHEET 2 AA5 2 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 AA6 3 ASN A 906 ASP A 908 0 SHEET 2 AA6 3 PRO A 897 ILE A 899 -1 N VAL A 898 O ILE A 907 SHEET 3 AA6 3 THR A 935 PRO A 936 -1 O THR A 935 N ILE A 899 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MASTER 389 0 0 53 22 0 0 6 9310 5 0 104 END