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(-) Description

Title :  STRUCTURAL BASIS FOR DNA STRAND SEPARATION BY A HEXAMERIC REPLICATIVE HELICASE
 
Authors :  Y. Chaban, J. A. Stead, K. Ryzhenkova, F. Whelan, K. Lamber, F. Antson, C. M. Sanders, E. V. Orlova
Date :  21 Jul 15  (Deposition) - 26 Aug 15  (Release) - 07 Oct 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  19.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Hydrolase, Dna Replication Fork (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Chaban, J. A. Stead, K. Ryzhenkova, F. Whelan, K. Lamber, A. Antson, C. M. Sanders, E. V. Orlova
Structural Basis For Dna Strand Separation By A Hexameric Replicative Helicase.
Nucleic Acids Res. V. 43 8551 2015
PubMed-ID: 26240379  |  Reference-DOI: 10.1093/NAR/GKV778

(-) Compounds

Molecule 1 - REPLICATION PROTEIN E1
    Chains: A, B, C, D, E, F
    EC Number: 3.6.4.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: COLE1
    Fragment: HELICASE DOMAIN, RESIDUES 301-605
    Organ: NUCLEUS
    Organism Scientific: BOVINE PAPILLOMAVIRUS
    Organism Taxid: 10571
    Synonym: 3.6.4.12, ATP-DEPENDENT HELICASE E1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2PO49Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:436 , THR A:437 , GLY A:438 , LYS A:439 , SER A:440 , PO4 A:1581 , MG A:1582BINDING SITE FOR RESIDUE PO4 A1580
02AC2SOFTWAREPRO A:435 , ASN A:436 , LYS A:439 , ASP A:479 , ASN A:523 , PO4 A:1580 , MG A:1582 , ARG B:538BINDING SITE FOR RESIDUE PO4 A1581
03AC3SOFTWARESER A:440 , ASP A:479 , PO4 A:1580 , PO4 A:1581 , ARG B:538BINDING SITE FOR RESIDUE MG A1582
04AC4SOFTWAREASN B:436 , THR B:437 , GLY B:438 , LYS B:439 , SER B:440 , MET B:441 , PO4 B:1580 , MG B:1581BINDING SITE FOR RESIDUE PO4 B1579
05AC5SOFTWAREPRO B:435 , ASN B:436 , LYS B:439 , ASP B:479 , ASN B:523 , PO4 B:1579 , MG B:1581 , ARG C:538BINDING SITE FOR RESIDUE PO4 B1580
06AC6SOFTWARESER B:440 , ASP B:479 , PO4 B:1579 , PO4 B:1580 , ARG C:538BINDING SITE FOR RESIDUE MG B1581
07AC7SOFTWAREASN C:436 , THR C:437 , GLY C:438 , LYS C:439 , SER C:440 , MET C:441 , PO4 C:1580 , MG C:1581BINDING SITE FOR RESIDUE PO4 C1579
08AC8SOFTWAREPRO C:435 , ASN C:436 , LYS C:439 , ASP C:479 , ASN C:523 , PO4 C:1579 , MG C:1581 , ARG D:538BINDING SITE FOR RESIDUE PO4 C1580
09AC9SOFTWARESER C:440 , ASP C:479 , PO4 C:1579 , PO4 C:1580BINDING SITE FOR RESIDUE MG C1581
10BC1SOFTWAREASN D:436 , THR D:437 , GLY D:438 , LYS D:439 , SER D:440BINDING SITE FOR RESIDUE PO4 D1580
11BC2SOFTWAREASN E:436 , THR E:437 , GLY E:438 , LYS E:439 , SER E:440 , TYR F:534BINDING SITE FOR RESIDUE PO4 E1579
12BC3SOFTWAREASN F:436 , THR F:437 , GLY F:438 , LYS F:439 , SER F:440BINDING SITE FOR RESIDUE PO4 F1580

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A9K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A9K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A9K)

(-) Exons   (0, 0)

(no "Exon" information available for 5A9K)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eeehhhhh.hhhhhhhhh....eeeeeehhhhhhhhhhh.hhhhhh..ee.........ee....eeeee......hhhhhhhh..eeeee.............hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a9k A 301 TLNESKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKHVKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCTDEQPFNITDADWKSFFVRLWGRLDLID 579
                                || 314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544     ||557       567       577  
                              305|                                                                                                                                                                                                                                             550|                         
                               310                                                                                                                                                                                                                                              554                         


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.ee.hhhhh.....hhhhhh...eee...hhhhhhhhhhhhhhhhhh.eeee.......eeee...eeeee......hhhhhhhh...eeee..........hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a9k B 301 TLNESKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKHVKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCTPFNITDADWKSFFVRLWGRLDLI 578
                                || 314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544    || 560       570        
                              305|                                                                                                                                                                                                                                            549|                      
                               310                                                                                                                                                                                                                                             556                      


Chain C from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eeehhhhh.....hhhhhh...eee...hhhhhhhhhhhhhhhhhh.eeee.......eeee...eeeee..hhhhhhhhhhhhhhheeee.........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a9k C 301 TLNESKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKHVKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCPFNITDADWKSFFVRLWGRLDLI 578
                                || 314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544   ||  561       571       
                              305|                                                                                                                                                                                                                                           548|                      
                               310                                                                                                                                                                                                                                            556                      


Chain D from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eeehhhhh.hhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh..eeee.......eeee...eeeee..hhhhhhhhhhhh...eeee...............hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a9k D 301 TLNESKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKHVKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCTESGEQPFNITDADWKSFFVRLWGRLDLID 579
                                || 314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544    || 555       565       575    
                              305|                                                                                                                                                                                                                                            549|                            
                               310                                                                                                                                                                                                                                             551                            


Chain E from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh..eee.......eee....eeeee......hhhhhhhh...eeee............hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a9k E 301 TLNESKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKHVKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCTDEPFNITDADWKSFFVRLWGRLDLI 578
                                || 314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544      |558       568       578
                              305|                                                                                                                                                                                                                                              551|                      
                               310                                                                                                                                                                                                                                               556                      


Chain F from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhh.eee...hhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh..eee.......eee....eeeee......hhhhhhhh...eeee..........hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a9k F 301 TLNESKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKHVKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCTPFNITDADWKSFFVRLWGRLDLID 579
                                || 314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544    || 560       570         
                              305|                                                                                                                                                                                                                                            549|                       
                               310                                                                                                                                                                                                                                             556
   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 5A9K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A9K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A9K)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        VE1_BPV1 | P03116: 1f08 1ksx 1ksy 2gxa 2v9p

(-) Related Entries Specified in the PDB File

5a9l STRUCTURAL BASIS FOR DNA STRAND SEPARATION BY A HEXAMERIC REPLICATIVE HELICASE
5a9m STRUCTURAL BASIS FOR DNA STRAND SEPARATION BY A HEXAMERIC REPLICATIVE HELICASE
5a9n STRUCTURAL BASIS FOR DNA STRAND SEPARATION BY A HEXAMERIC REPLICATIVE HELICASE
5a9o STRUCTURAL BASIS FOR DNA STRAND SEPARATION BY A HEXAMERIC REPLICATIVE HELICASE RELATED ID: EMD-3087 RELATED DB: EMDB