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(-) Description

Title :  STRUCTURE OF THE REV1 CTD-REV3/7-POL KAPPA RIR COMPLEX
 
Authors :  Jessica Wojtaszek, C. -J. Lee, P. Zhou
Date :  11 Jun 12  (Deposition) - 08 Aug 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Translesion Synthesis, Transferase -Dna Binding Protein Complex, Transferase-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wojtaszek, C. J. Lee, S. D'Souza, B. Minesinger, H. Kim, A. D. D'Andrea, G. C. Walker, P. Zhou
Structural Basis Of Rev1-Mediated Assembly Of A Quaternary Vertebrate Translesion Polymerase Complex Consisting Of Rev1, Heterodimeric Pol Zeta And Pol Kappa
J. Biol. Chem. V. 287 33836 2012
PubMed-ID: 22859295  |  Reference-DOI: 10.1074/JBC.M112.394841

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN REV1
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: REV1 C-TERMINAL DOMAIN
    Gene: REV1, REV1L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: REV1-LIKE TERMINAL DEOXYCYTIDYL TRANSFERASE
 
Molecule 2 - DNA POLYMERASE KAPPA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: REV1-INTERACTING REGION (RIR) OF POL KAPPA
    Gene: POLK, DINB1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DINB PROTEIN, DINP
 
Molecule 3 - MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2B
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: REV7
    Gene: MAD2L2, MAD2B, REV7
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MITOTIC ARREST DEFICIENT 2-LIKE PROTEIN 2, MAD2-LIKE PROTEIN 2
 
Molecule 4 - DNA POLYMERASE ZETA CATALYTIC SUBUNIT
    Chains: D
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: REV7-INTERACTING REGION OF REV3
    Gene: REV3L, POLZ, SEZ4
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PROTEIN REVERSIONLESS 3-LIKE, REV3-LIKE, SEIZURE-RELATED PROTEIN 4

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO48Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO48Ligand/IonPHOSPHATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:1167 , LYS A:1171 , TYR A:1210 , ARG A:1213BINDING SITE FOR RESIDUE GOL A 1301
2AC2SOFTWAREGLU C:81 , LYS C:82 , HIS C:151 , ARG D:1870 , HIS D:1873BINDING SITE FOR RESIDUE PO4 C 301
3AC3SOFTWAREASP A:1228 , ASP A:1232 , HIS C:180 , MET C:181 , HOH C:403 , HOH C:458 , ARG D:1870BINDING SITE FOR RESIDUE PO4 C 302
4AC4SOFTWAREHIS C:118 , SER C:194 , ASP C:195 , ILE C:196BINDING SITE FOR RESIDUE PO4 C 303
5AC5SOFTWARELEU A:1231 , GLN A:1235 , HIS C:182 , ASP C:183 , PO4 C:307BINDING SITE FOR RESIDUE PO4 C 304
6AC6SOFTWAREMET C:1 , TYR C:32 , VAL C:33 , GLU C:35 , VAL C:39 , ASP C:134BINDING SITE FOR RESIDUE PO4 C 305
7AC7SOFTWAREASN C:10 , GLU C:76 , LYS C:77 , HOH C:444BINDING SITE FOR RESIDUE PO4 C 306
8AC8SOFTWAREVAL A:1248 , HIS C:180 , HIS C:182 , PO4 C:304BINDING SITE FOR RESIDUE PO4 C 307
9AC9SOFTWAREGLU A:1202 , ASP A:1205 , HOH A:1418 , LYS C:129 , PRO C:188 , LEU C:189BINDING SITE FOR RESIDUE PO4 C 308

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FJO)

(-) 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:97
                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                4fjo A 1153 AAPNLAGAVEFSDVKTLLKEWITTISDPMEEDILQVVRYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT 1249
                                  1162      1172      1182      1192      1202      1212      1222      1232      1242       


Chain B from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                4fjo B  565 SFFDKKRSER  574
                                   574


Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee...hhhhhhhh.......eee.hhhhhh...eeeeeeeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4fjo C    1 MTTLTRQDLNFGQVVADVLSEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSINSDSLLSHVEQLLAAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKN  210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210


Chain D from PDB  Type:PROTEIN  Length:30
                                                               
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ....hhhh.eeee.....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                4fjo D 1865 GSFTPRTAHILKPLMSPPSREEIVATLLDH 1894
                                  1874      1884      1894
   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 4FJO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 73)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        POLK_MOUSE | Q9QUG2: 2lsj
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(-) Related Entries Specified in the PDB File

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