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(-) Description

Title :  JC POLYOMAVIRUS VP1 FIVE-FOLD PORE MUTANT N221W
 
Authors :  L. J. Stroh, T. Stehle
Date :  09 Sep 14  (Deposition) - 18 Feb 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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: 15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-290
    Mutation: YES
    Organism Common: JCPYV
    Organism Scientific: JC POLYOMAVIRUS
    Organism Taxid: 10632
    Synonym: MAJOR STRUCTURAL PROTEIN VP1, MAD-1 VP1

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2GOL14Ligand/IonGLYCEROL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:224 , VAL A:225 , GOL A:302 , HOH A:422 , HOH A:472 , HOH A:499binding site for residue GOL A 301
02AC2SOFTWAREHIS A:142 , VAL A:225 , LEU A:226 , HIS A:227 , ARG A:276 , GOL A:301 , HOH A:516 , HOH A:558binding site for residue GOL A 302
03AC3SOFTWAREGLY A:138 , THR A:139 , GLY A:219 , GLU A:220 , MET A:261 , HOH A:432 , VAL E:120 , GLY E:133 , PRO E:135binding site for residue GOL A 303
04AC4SOFTWARESER A:62 , SER A:64 , SER A:69 , ASP A:70 , SER A:71 , MET A:76 , HOH A:535 , HIS E:121binding site for residue GOL A 304
05AC5SOFTWAREGLU A:38 , LYS A:108 , LYS A:279 , GLN A:281 , HOH A:575binding site for residue EDO A 305
06AC6SOFTWAREVAL A:120 , THR A:127 , GLY A:133 , PRO A:135 , GLY B:138 , THR B:139 , GLY B:219 , GLU B:220 , HOH B:422binding site for residue GOL B 301
07AC7SOFTWAREHIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72 , HOH B:405binding site for residue GOL B 302
08AC8SOFTWAREHIS B:142 , LEU B:226 , HIS B:227 , ARG B:276binding site for residue EDO B 303
09AC9SOFTWAREHIS B:142 , PHE B:213 , GLY B:214 , THR B:215 , HOH B:440binding site for residue EDO B 304
10AD1SOFTWAREHIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , PRO C:72 , HOH C:557binding site for residue GOL C 301
11AD2SOFTWAREVAL B:120 , GLY B:133 , PRO B:135 , GLY C:138 , THR C:139 , GLY C:219 , GLU C:220 , HOH C:411binding site for residue GOL C 302
12AD3SOFTWAREGLU C:208 , ASN C:209 , ARG C:211 , ASP C:238 , GLY C:243binding site for residue EDO C 303
13AD4SOFTWAREHIS C:142 , GLY C:214 , THR C:215binding site for residue EDO C 304
14AD5SOFTWAREHIS 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
15AD6SOFTWAREVAL D:120 , THR D:127 , GLY D:133 , PRO D:135 , HOH D:427 , GLY E:138 , THR E:139 , GLY E:219 , GLU E:220 , MET E:261binding site for residue GOL D 302
16AD7SOFTWAREVAL C:120 , GLY C:133 , PRO C:135 , THR D:139 , GLU D:220 , HOH D:429binding site for residue GOL D 303
17AD8SOFTWAREHIS D:142 , VAL D:225 , LEU D:226 , HIS D:227 , ARG D:276 , EDO D:305 , HOH D:545 , HOH D:549binding site for residue GOL D 304
18AD9SOFTWAREHIS D:142 , GLY D:214 , THR D:215 , GOL D:304 , HOH D:496binding site for residue EDO D 305
19AE1SOFTWAREHIS E:142 , LEU E:226 , HIS E:227 , EDO E:303 , HOH E:560 , HOH E:562binding site for residue GOL E 301
20AE2SOFTWAREASP 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:401 , HOH E:403binding site for residue GOL E 302
21AE3SOFTWAREHIS E:142 , GLY E:214 , THR E:215 , GOL E:301 , HOH E:441binding site for residue EDO E 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WDZ)

(-) 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..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
                 4wdz A  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGEWVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 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 .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
                 4wdz B  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGEWVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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:257
                                                                                                                                                                                                                                                                                                 
               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
                 4wdz C  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGEWVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 288
                                    34        44        54        64        74        84      |101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       
                                                                                             91|                                                                                                                                                                                             
                                                                                              99                                                                                                                                                                                             


Chain D 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...eeeee...................hhhhhh.....eeee......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wdz D  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGEWVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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 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..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
                 4wdz E  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGEWVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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)
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  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 '|'

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(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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
        VP1_POVJC | P03089: 3nxd 3nxg 4jcd 4jce 4jcf 4wdy 4we0 4x14 4x15 4x16 4x17

(-) Related Entries Specified in the PDB File

3nxd JC POLYOMAVIRUS MAD1 VP1