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(-) Description

Title :  JC POLYOMAVIRUS VP1 FIVE-FOLD PORE MUTANT P223M
 
Authors :  L. J. Stroh, T. Stehle
Date :  09 Sep 14  (Deposition) - 18 Feb 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Beta-Sandwich, Jelly-Roll, Viral Major Capsid Protein, Five-Fold Pore, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Nelson, L. J. Stroh, G. V. Gee, B. A. O'Hara, T. Stehle, W. J. Atwood
Modulation Of A Pore In The Capsid Of Jc Polyomavirus Reduces Infectivity And Prevents Exposure Of The Minor Capsid Proteins.
J. Virol. V. 89 3910 2015
PubMed-ID: 25609820  |  Reference-DOI: 10.1128/JVI.00089-15

(-) Compounds

Molecule 1 - MAJOR CAPSID PROTEIN VP1
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: JCPYV
    Organism Scientific: JC POLYOMAVIRUS
    Organism Taxid: 10632
    Synonym: MAJOR STRUCTURAL PROTEIN VP1

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:62 , SER A:64 , SER A:69 , ASP A:70 , SER A:71 , PRO A:72 , HIS E:121binding site for residue GOL A 301
2AC2SOFTWAREHIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72 , HOH B:403binding site for residue GOL B 301
3AC3SOFTWAREHIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , MET C:76binding site for residue GOL C 301
4AC4SOFTWAREGLY C:214 , THR C:215 , HOH C:485binding site for residue EDO C 302
5AC5SOFTWAREHIS C:121 , SER D:62 , SER D:64 , SER D:69 , ASP D:70 , SER D:71 , PRO D:72binding site for residue GOL D 301
6AC6SOFTWAREHIS D:142 , THR D:215binding site for residue EDO D 302
7AC7SOFTWAREARG A:265 , ASP B:65 , HIS D:121 , SER E:62 , SER E:64 , SER E:69 , ASP E:70 , SER E:71 , PRO E:72 , HOH E:408binding site for residue GOL E 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WE0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WE0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WE0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WE0)

(-) Exons   (0, 0)

(no "Exon" information available for 4WE0)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeeeee......................hhhhh..hhhhh...eeeeee......eeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4we0 A  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVMPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 289
                                    33        43        53        63        73        83       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         
                                                                                              91|                                                                                                                                                                                              
                                                                                               99                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..hhh.eeeeeeee.............................hhhhh...eeeeee......eeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4we0 B  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVMPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 288
                                    33        43        53        63        73        83       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
                                                                                              91|                                                                                                                                                                                             
                                                                                               99                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhh.eeeeeeee.............................hhhhh...eeeeee.....eeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4we0 C  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVMPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 288
                                    34        44        54        64        74        84     ||102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
                                                                                            90|                                                                                                                                                                                             
                                                                                             99                                                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhh.eeeeeeee.............................hhhhh...eeeeee.....eeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4we0 D  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVMPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 288
                                    33        43        53        63        73        83      |101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       
                                                                                             90|                                                                                                                                                                                             
                                                                                              99                                                                                                                                                                                             


Chain E from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhh.eeeeeeee.............................hhhhh...eeeeee......eeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4we0 E  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVMPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 288
                                    33        43        53        63        73        83       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
                                                                                              91|                                                                                                                                                                                             
                                                                                               99
   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 4WE0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WE0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WE0)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  VP1_POVJC | P03089
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 Related Entries

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

UniProtKB/Swiss-Prot
        VP1_POVJC | P03089: 3nxd 3nxg 4jcd 4jce 4jcf 4wdy 4wdz 4x14 4x15 4x16 4x17

(-) Related Entries Specified in the PDB File

3nxd JC POLYOMAVIRUS MAD-1 VP1