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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN REV3-REV7-REV1-POLKAPPA COMPLEX
 
Authors :  J. Tao, X. Min, X. Wei
Date :  10 Aug 12  (Deposition) - 13 Mar 13  (Release) - 13 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A (1x),C (1x),E (1x),G (1x)
Biol. Unit 2:  B (1x),D (1x),F (1x)
Keywords :  Translesion Polymerases Complex, Four-Helix Bundle, Beta-Hairpin Domain, Anti-Parallel Sheets, Translesion Dna Synthesis, Polymerase Switch, None, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Xie, X. Yang, M. Xu, T. Jiang
Structural Insights Into The Assembly Of Human Translesion Polymerase Complexes
Protein Cell V. 3 864 2012
PubMed-ID: 23143872  |  Reference-DOI: 10.1007/S13238-012-2102-X

(-) Compounds

Molecule 1 - MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAD2L2, MAD2B, REV7
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MITOTIC ARREST DEFICIENT 2-LIKE PROTEIN 2, MAD2-LIKE PROTEIN 2, REV7 HOMOLOG, HREV7
 
Molecule 2 - DNA POLYMERASE ZETA CATALYTIC SUBUNIT
    Chains: C, D
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: REV7-BINDING DOMAIN, UNP RESIDUES 1874-1893
    Gene: REV3L, POLZ, REV3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN REVERSIONLESS 3-LIKE, REV3-LIKE, HREV3
 
Molecule 3 - DNA REPAIR PROTEIN REV1
    Chains: E, F
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 1117-1251
    Gene: REV1, REV1L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA INTEGRIN-BINDING PROTEIN 80, AIBP80, REV1-LIKE TERMINAL DEOXYCYTIDYL TRANSFERASE
 
Molecule 4 - DNA POLYMERASE KAPPA
    Chains: G
    EC Number: 2.7.7.7
    Engineered: YES
    Fragment: POLKAPPA RIR PEPTIDE, UNP RESIDUES 564-573
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synonym: DINB PROTEIN, DINP
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): A (1x) C (1x) E (1x) G (1x)
Biological Unit 2 (1x):  B (1x) D (1x) F (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4GK5)

(-) Sites  (0, 0)

(no "Site" information available for 4GK5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GK5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GK5)

(-) Exons   (0, 0)

(no "Exon" information available for 4GK5)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee...hhhhhhhhh......eee.hhhhhh...eeeeeeeee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4gk5 A    9 LNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPISSDSLLSHVEQLLAAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHK  209
                                    18        28        38        48        58        68        78        88        98       111       121       131       141       151       161       171       181       191       201        
                                                                                                                           106|                                                                                                   
                                                                                                                            110                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeee.......hhhhhhhhhhhhhhhhhh........eeeeeeee...hhhhhhhhh......eee.hhhhhh....eeeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gk5 B   10 NFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQSLLSHVEQLLAAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAH  208
                                    19        29        39        49        59        69        79        89        99    || 118       128       138       148       158       168       178       188       198       208
                                                                                                                        104|                                                                                              
                                                                                                                         114                                                                                              


Chain C from PDB  Type:PROTEIN  Length:20
                                                     
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...eeee......hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                4gk5 C 1874 TANILKPLMSPPSREEIMAT 1893
                                  1883      1893


Chain D from PDB  Type:PROTEIN  Length:20
                                                     
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                4gk5 D 1874 TANILKPLMSPPSREEIMAT 1893
                                  1883      1893


Chain E from PDB  Type:PROTEIN  Length:96
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                4gk5 E 1156 APNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT 1251
                                  1165      1175      1185      1195      1205      1215      1225      1235      1245      


Chain F from PDB  Type:PROTEIN  Length:93
                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                4gk5 F 1156 APNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVWNMAFDFILDNVQVVLQQTYGSTLKVT 1251
                                  1165      1175      1185      1195      1205      1215   || 1228      1238      1248   
                                                                                        1219|                            
                                                                                         1223                            


Chain G from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                4gk5 G  566 SFFDKKRS  573
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4GK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GK5)

(-) Gene Ontology  (57, 89)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MD2L2_HUMAN | Q9UI95: 3abd 3abe 3vu7 4ext 4gk0
        POLK_HUMAN | Q9UBT6: 1t94 2lsi 2oh2 2w7o 2w7p 3in5 3pzp 4ba9 4u6p 4u7c 5t14
        REV1_HUMAN | Q9UBZ9: 2ebw 2lsi 2lsk 2lsy 2n1g 3gqc 3vu7 4ba9 4ext 4gk0
        REV3L_HUMAN | O60673: 3abd 3abe 3vu7 4ext 4gk0

(-) Related Entries Specified in the PDB File

4gk0 THE SAME PROTEINS COMPLEXED WITH POLKAPPA RIR PEPTIDE