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(-) Description

Title :  CORE MODEL OF THE MOUSE MAMMARY TUMOR VIRUS INTASOME
 
Authors :  D. L. Lyumkis, A. Ballandras-Colas, M. Brown, N. J. Cook, T. G. Dewdney, B. Demeler, P. Cherepanov, A. N. Engelman
Date :  24 Nov 15  (Deposition) - 17 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Integration, Retrovirus, Integrase, Intasome, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ballandras-Colas, M. Brown, N. J. Cook, T. G. Dewdney, B. Demeler, P. Cherepanov, D. Lyumkis, A. N. Engelman
Cryo-Em Reveals A Novel Octameric Integrase Structure For Betaretroviral Intasome Function
Nature V. 530 358 2016
PubMed: search  |  Reference-DOI: 10.1038/NATURE16955

(-) Compounds

Molecule 1 - INTEGRASE
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: PC2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1437-1701
    Organism Common: MMTV
    Organism Scientific: MOUSE MAMMARY TUMOR VIRUS
    Organism Taxid: 11757
 
Molecule 2 - INTEGRASE
    Chains: C, D, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: PC2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 1653-1701)
    Organism Common: MMTV
    Organism Scientific: MOUSE MAMMARY TUMOR VIRUS
    Organism Taxid: 11757
 
Molecule 3 - 5'-D(*AP*AP*TP*GP*CP*CP*GP*CP*AP*GP*TP*CP*GP*GP*CP*CP*GP*AP *CP*CP*TP*G)-3'
    Chains: I, K
    Engineered: YES
    Organism Scientific: MOUSE MAMMARY TUMOR VIRUS
    Organism Taxid: 11757
    Other Details: PRE-CLEAVED VIRAL DNA 3' STRAND
    Synthetic: YES
 
Molecule 4 - 5'-D(*CP*AP*GP*GP*TP*CP*GP*GP*CP*CP*GP*AP*CP*TP*GP*CP*GP*GP *CP*A)-3'
    Chains: J, L
    Engineered: YES
    Organism Scientific: MOUSE MAMMARY TUMOR VIRUS
    Organism Taxid: 11757
    Other Details: PRE-CLEAVED VIRAL DNA 5' STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit : ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , HIS A:13 , CYS A:37 , CYS A:40BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS B:9 , HIS B:13 , CYS B:37 , CYS B:40BINDING SITE FOR RESIDUE ZN B 500
3AC3SOFTWAREHIS E:9 , HIS E:13 , CYS E:37 , CYS E:40BINDING SITE FOR RESIDUE ZN E 500
4AC4SOFTWAREHIS F:9 , HIS F:13 , CYS F:37 , ASN F:39 , CYS F:40BINDING SITE FOR RESIDUE ZN F 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JCA)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:231 -Pro A:232
2Gly B:231 -Pro B:232
3Gly C:231 -Pro C:232
4Gly D:231 -Pro D:232
5Gly E:231 -Pro E:232
6Gly F:231 -Pro F:232
7Gly G:231 -Pro G:232
8Gly H:231 -Pro H:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JCA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JCA)

(-) Exons   (0, 0)

(no "Exon" information available for 3JCA)

(-) Sequences/Alignments

Asymmetric/Biological 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh.....................eeeeee..hhhhhhhheeeeeee....eeeeeee...hhhhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhh........eeeee......eeeeeeeeeee..eeee........eeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jca A   1 ALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCPHAPQLGVNPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWGPISADPKPMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                    10        20        30        40||      53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
                                                                   41|                                                                                                                                                                                                                            
                                                                    45                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh............eeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhh........eeeee......eeeeeeeeeee..eeee........eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jca B   1 ALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWGPISADPKPMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                    10        20        30        40||      62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262   
                                                                   41|                                                                                                                                                                                                                   
                                                                    54                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeeeeeeee..eeee........eeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3jca C 217 PMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                   226       236       246       256         


Chain D from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeeeeeeee..eeee........eeee...ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3jca D 217 PMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                   226       236       246       256         


Chain E from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh.....................eeeeee..hhhhhhhheeeeeee....eeeeeee...hhhhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.......hhhhhhhh........eeeee......eeeeeeeeeee..eeee........eeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jca E   1 ALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCPHAPQLGVNPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWGPISADPKPMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                    10        20        30        40||      53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
                                                                   41|                                                                                                                                                                                                                            
                                                                    45                                                                                                                                                                                                                            


Chain F from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhh............eeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhh........eeeee......eeeeeeeeeee..eeee........eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jca F   1 ALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWGPISADPKPMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                    10        20        30        40||      62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262   
                                                                   41|                                                                                                                                                                                                                   
                                                                    54                                                                                                                                                                                                                   


Chain G from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeeeeeeee..eeee........eeee...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3jca G 217 PMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                   226       236       246       256         


Chain H from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeeeeeeee..eeee........eeee...ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 3jca H 217 PMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAESPIWVPDRFIRPFT 265
                                   226       236       246       256         


Chain I from PDB  Type:DNA  Length:21
                                                     
                 3jca I   1 AATGCCGCAGTCGGCCGACCT  21
                                    10        20 


Chain J from PDB  Type:DNA  Length:19
                                                   
                 3jca J   2 AGGTCGGCCGACTGCGGCA  20
                                    11         


Chain K from PDB  Type:DNA  Length:21
                                                     
                 3jca K   1 AATGCCGCAGTCGGCCGACCT  21
                                    10        20 


Chain L from PDB  Type:DNA  Length:19
                                                   
                 3jca L   2 AGGTCGGCCGACTGCGGCA  20
                                    11
   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 3JCA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JCA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JCA)

(-) Gene Ontology  (21, 36)

Asymmetric/Biological Unit(hide GO term definitions)

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  3jca
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  POL_MMTVB | P03365
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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_MMTVB | P03365: 5cz1 5cz2 5d7u

(-) Related Entries Specified in the PDB File

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