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(-) Description

Title :  S268Y VARIANT OF JC POLYOMAVIRUS MAJOR CAPSID PROTEIN VP1
 
Authors :  T. Stehle, L. J. Stroh
Date :  21 Feb 13  (Deposition) - 14 Aug 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Beta-Sandwich, Jelly Roll Topology, Viral Protein, Major Capsid Protein, Pml-Associated Vp1 Mutation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Maginnis, L. J. Stroh, G. V. Gee, B. A. O'Hara, A. Derdowski, T. Stehle, W. J. Atwood
Progressive Multifocal Leukoencephalopathy-Associated Mutations In The Jc Polyomavirus Capsid Disrupt Lactoseries Tetrasaccharide C Binding.
Mbio V. 4 00247 2013
PubMed-ID: 23760462  |  Reference-DOI: 10.1128/MBIO.00247-13

(-) Compounds

Molecule 1 - MAJOR CAPSID PROTEIN VP1
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    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, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:62 , SER A:64 , SER A:69 , ASP A:70 , SER A:71 , PRO A:72 , HOH A:515 , HIS E:121BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWAREHIS A:142 , GLY A:214 , THR A:215 , HOH A:561BINDING SITE FOR RESIDUE EDO A 302
3AC3SOFTWAREHIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , MET B:76BINDING SITE FOR RESIDUE GOL B 301
4AC4SOFTWAREHIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , PRO C:72 , HOH C:543BINDING SITE FOR RESIDUE GOL C 301
5AC5SOFTWAREHIS C:121 , SER D:62 , SER D:64 , ASP D:70 , SER D:71 , PRO D:72 , HOH D:558BINDING SITE FOR RESIDUE GOL D 301
6AC6SOFTWAREHIS D:142 , GLY D:214 , THR D:215 , HOH D:448BINDING SITE FOR RESIDUE EDO D 302
7AC7SOFTWAREARG A:265 , HOH A:600 , ASP B:65 , THR B:66 , HIS D:121 , SER E:62 , SER E:64 , SER E:69 , ASP E:70 , SER E:71 , PRO E:72 , HOH E:491BINDING SITE FOR RESIDUE GOL E 301
8AC8SOFTWAREHIS E:142 , GLY E:214 , THR E:215 , HOH E:417BINDING SITE FOR RESIDUE EDO E 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JCD)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4jcda_ A: automated matches                                                                                                                                                                                                                                      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
                 4jcd A  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGYQQWRGLSRYFKVQLRKRRVK 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 B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains d4jcdb_ B: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhh.eeeeeeee.............................hhhhh...eeeeee.....eeeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jcd B  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGYQQWRGLSRYFKVQLRKRRVK 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        
                                                                                             90|                                                                                                                                                                                              
                                                                                              98                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4jcdc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhh.eeeeeeee......................hhhhh..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
                 4jcd C  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGYQQWRGLSRYFKVQLRKRRVK 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 d4jcdd_ D: automated matches                                                                                                                                                                                                                                      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
                 4jcd D  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGYQQWRGLSRYFKVQLRKRRVK 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4jcde_ E: automated matches                                                                                                                                                                                                                                      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
                 4jcd E  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGYQQWRGLSRYFKVQLRKRRVK 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
   Legend:   → Mismatch (orange background)
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    → 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, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4jce 4jcf 4wdy 4wdz 4we0 4x14 4x15 4x16 4x17

(-) Related Entries Specified in the PDB File

3nxd WILD TYPE JC POLYOMAVIRUS VP1 IN COMPLEX WITH LSTC
3nxg WILD TYPE JC POLYOMAVIRUS VP1
4jce
4jcf