Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HALOFERAX VOLCANII PROLIFERATING CELL NUCLEAR ANTIGEN
 
Authors :  J. A. Winter, P. Christofi, S. Morroll, K. A. Bunting
Date :  26 Jul 09  (Deposition) - 01 Sep 09  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Processivity Factor, Sliding Clamp, Halophilic, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Winter, P. Christofi, S. Morroll, K. A. Bunting
The Crystal Structure Of Haloferax Volcanii Proliferating Cell Nuclear Antigen Reveals Unique Surface Charge Characteristics Due To Halophilic Adaptation
Bmc Struct. Biol. V. 9 55 2009
PubMed-ID: 19698123  |  Reference-DOI: 10.1186/1472-6807-9-55

(-) Compounds

Molecule 1 - PCNA
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC11 184-11B
    Expression System Strain: B834 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PCNA
    Organism Common: HALOFERAX VOLCANII
    Organism Scientific: HALOFERAX VOLCANII
    Organism Taxid: 2246
    Synonym: PROLIFERATING CELL NUCLEAR ANTIGEN PCNA

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1NA9Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:150 , HOH A:264 , HOH A:294 , HOH A:321 , HOH A:324 , HOH A:325BINDING SITE FOR RESIDUE NA A 401
2AC2SOFTWAREASP A:146 , SER A:149 , ASP A:150 , HOH A:257 , HOH A:294BINDING SITE FOR RESIDUE NA A 402
3AC3SOFTWARELEU A:127 , HOH A:258 , HOH A:261 , HOH A:304BINDING SITE FOR RESIDUE NA A 403
4AC4SOFTWAREASP B:150 , HOH B:248 , HOH B:249 , HOH B:253 , HOH B:265 , HOH B:269 , NA B:405BINDING SITE FOR RESIDUE NA B 404
5AC5SOFTWAREASP B:146 , SER B:149 , ASP B:150 , HOH B:253 , HOH B:291 , NA B:404BINDING SITE FOR RESIDUE NA B 405
6AC6SOFTWARELEU B:127 , HOH B:259 , HOH B:260BINDING SITE FOR RESIDUE NA B 406
7AC7SOFTWAREASP C:150 , HOH C:252 , HOH C:266 , HOH C:286 , HOH C:287 , HOH C:357BINDING SITE FOR RESIDUE NA C 407
8AC8SOFTWAREASP C:146 , SER C:149 , ASP C:150 , HOH C:286BINDING SITE FOR RESIDUE NA C 408
9AC9SOFTWARELEU C:127 , HOH C:256 , HOH C:257 , HOH C:282 , HOH C:325BINDING SITE FOR RESIDUE NA C 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IFV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IFV)

(-) 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:216
 aligned with D0VWY8_HALVO | D0VWY8 from UniProtKB/TrEMBL  Length:247

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         D0VWY8_HALVO     2 FKAIVSAATLRDALDSVSVLVDECKIRLNEESLSIRAVDPANVGMVDLTLDAAAFESYEAHGGVIGVNLSRLEEVAGMAGAGDLIHLTLDEETRKLNIRIDGLSYTLALIDPDSIRQEPDIPDLDLAANIVLEGTHLDRGIKAADMVSDHIRLRVDGAEETFHIEAEGDTDDVDLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPR 243
               SCOP domains d3ifva1 A:2-112 Proliferati   ng cell nuclear antigen (PCN     A)                                              d3i    fva2 A:113-243 Proliferating cell nuclear antigen (PCNA)                                                                     SCOP domains
               CATH domains 3ifvA00 A:2-243  [code=3.70   .10.10, no name defined]                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhh....eee.---.eeeeeee.....eeeeeeee.hhh...-----.eeehhhhhhhhhh..----.eee.-------.eeee..eeee.---....----.........eeeeeehhhhhhhhhhhhhhh.eeeeeee....eeeeeee....eeeeeehhhhh.eeee...eeeeehhhhhhhhhhh....eeeeee.....eeeeeeehhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ifv A   2 FKAIVSAATLRDALDSVSVLVDECKIR---ESLSIRAVDPANVGMVDLTLDAAAFESY-----VIGVNLSRLEEVAGMA----LIHLT-------LNIRIDGLSYTL---DPDS----PDIPDLDLAANIVLEGTHLDRGIKAADMVSDHIRLRVDGAEETFHIEAEGDTDDVDLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPR 243
                                    11        21      |  -|       41        51       | -   |    71        |-   |   | -     | 101      |  -|  |   121       131       141       151       161       171       181       191       201       211       221       231       241  
                                                     28  32                         59    65             80   85  89      97        108 112  |  120                                                                                                                           
                                                                                                                                           115                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with D0VWY8_HALVO | D0VWY8 from UniProtKB/TrEMBL  Length:247

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         D0VWY8_HALVO     2 FKAIVSAATLRDALDSVSVLVDECKIRLNEESLSIRAVDPANVGMVDLTLDAAAFESYEAHGGVIGVNLSRLEEVAGMAGAGDLIHLTLDEETRKLNIRIDGLSYTLALIDPDSIRQEPDIPDLDLAANIVLEGTHLDRGIKAADMVSDHIRLRVDGAEETFHIEAEGDTDDVDLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPR 243
               SCOP domains d3ifvb1 B:2-112 Proliferating cell nuclear antigen (PCNA)                                                      d3ifvb2 B:1   13-243 Proliferating cell nuclear antigen (PCNA)                                                                      SCOP domains
               CATH domains 3ifvB00 B:2-243  [code=3.70.10.10, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh...eeeeee...eeeeeee.....eeeeeeee.hhh.eee....eeeeehhhhhhhhh......eeeee.-----.eeeee..eeeee...hhhhh.......---..eeeeeehhhhhhhhhhhhh...eeeeeee....eeeeeee....eeeeeehhhhh.eee...eeeeeehhhhhhhhhhh....eeeeee.....eeeeeeehhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ifv B   2 FKAIVSAATLRDALDSVSVLVDECKIRLNEESLSIRAVDPANVGMVDLTLDAAAFESYEAHGGVIGVNLSRLEEVAGMAGAGDLIHLTL-----KLNIRIDGLSYTLALIDPDSIRQEPDIP---LAANIVLEGTHLDRGIKAADMVSDHIRLRVDGAEETFHIEAEGDTDDVDLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPR 243
                                    11        21        31        41        51        61        71        81        |-    |  101       111       121 |   | 131       141       151       161       171       181       191       201       211       221       231       241  
                                                                                                                   90    96                        123 127                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:240
 aligned with D0VWY8_HALVO | D0VWY8 from UniProtKB/TrEMBL  Length:247

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
         D0VWY8_HALVO     2 FKAIVSAATLRDALDSVSVLVDECKIRLNEESLSIRAVDPANVGMVDLTLDAAAFESYEAHGGVIGVNLSRLEEVAGMAGAGDLIHLTLDEETRKLNIRIDGLSYTLALIDPDSIRQEPDIPDLDLAANIVLEGTHLDRGIKAADMVSDHIRLRVDGAEETFHIEAEGDTDDVDLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPR 243
               SCOP domains d3ifvc1 C:2-112 Proliferating cell nuclear antigen (PCNA)                                                      d3ifvc2 C:113-243 Proliferating cell nuclear antigen (PCNA)                                                                         SCOP domains
               CATH domains 3ifvC00 C:2-243  [code=3.70.10.10, no name defined]                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh...eeeeee...eeeeeee.....eeeeeeee.hhh.eee...eeeeeehhhhhhhhh..--..eeeeeee....eeeeee..eeeeee..hhhhh............eeeeeehhhhhhhhhhhhhhh.eeeeeee....eeeeeee....eeeeeehhhhh.eeee...eeeeehhhhhhhhhhh....eeeeee.....eeeeeeehhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ifv C   2 FKAIVSAATLRDALDSVSVLVDECKIRLNEESLSIRAVDPANVGMVDLTLDAAAFESYEAHGGVIGVNLSRLEEVAGMA--GDLIHLTLDEETRKLNIRIDGLSYTLALIDPDSIRQEPDIPDLDLAANIVLEGTHLDRGIKAADMVSDHIRLRVDGAEETFHIEAEGDTDDVDLSLPPADLISIEAGAADSLFSLDYLKDMNKAIPTDAEVTVELGEEFPVKLHYQIAEGMGTITYMLAPR 243
                                    11        21        31        41        51        61        71        |- |      91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
                                                                                                         80 83
   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  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (D0VWY8_HALVO | D0VWY8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030337    DNA polymerase processivity factor activity    An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ifv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ifv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  D0VWY8_HALVO | D0VWY8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  D0VWY8_HALVO | D0VWY8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D0VWY8_HALVO | D0VWY8: 3hi8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3IFV)