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(-) Description

Title :  UNLIGANDED BK POLYOMAVIRUS VP1 PENTAMER
 
Authors :  U. Neu, L. J. Stroh, T. Stehle
Date :  03 Sep 13  (Deposition) - 06 Nov 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Antiparallel Beta Sandwich, Jelly-Roll Topology, Viral Protein, Polyomavirus, Receptor Switch, Virus Major Capsid Protein, Attachment To Host-Cell Surface Receptors (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Neu, S. A. Allen, B. S. Blaum, Y. Liu, M. Frank, A. S. Palma, L. J. Stroh T. Feizi, T. Peters, W. J. Atwood, T. Stehle
A Structure-Guided Mutation In The Major Capsid Protein Retargets Bk Polyomavirus.
Plos Pathog. V. 9 03688 2013
PubMed-ID: 24130487  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003688

(-) Compounds

Molecule 1 - VP1 CAPSID PROTEIN
    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
    Organism Common: BKPYV
    Organism Scientific: BK POLYOMAVIRUS
    Organism Taxid: 10629

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:150 , GLY A:222 , THR A:223 , HOH A:571BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWARELYS A:180 , HIS A:193BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWAREHIS B:150 , GLY B:222 , THR B:223 , HOH B:538BINDING SITE FOR RESIDUE GOL B 401
04AC4SOFTWARELYS B:180 , HIS B:193BINDING SITE FOR RESIDUE CL B 402
05AC5SOFTWAREHIS C:150 , GLY C:222 , THR C:223 , HOH C:503 , HOH C:540BINDING SITE FOR RESIDUE GOL C 401
06AC6SOFTWAREPRO C:179 , LYS C:180 , HIS C:193BINDING SITE FOR RESIDUE CL C 402
07AC7SOFTWAREHIS D:150 , PHE D:152 , GLY D:222 , THR D:223 , HOH D:591 , HOH D:680BINDING SITE FOR RESIDUE GOL D 401
08AC8SOFTWAREPRO D:179 , LYS D:180 , HIS D:193BINDING SITE FOR RESIDUE CL D 402
09AC9SOFTWAREHIS E:150 , PHE E:152 , GLY E:222 , THR E:223 , HOH E:564BINDING SITE FOR RESIDUE GOL E 401
10BC1SOFTWAREPRO E:179 , LYS E:180 , HIS E:193BINDING SITE FOR RESIDUE CL E 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MJ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MJ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4MJ1)

(-) 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 d4mj1a_ A: automated matches                                                                                                                                                                                                                                        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..............eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj1 A  33 EVLEVKTGVDAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVK 296
                                    42        52        62        72        82        92       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287         
                                                                                              101|                                                                                                                                                                                             
                                                                                               107                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains d4mj1b_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.eeeeeeee......................hhhhh..hhhhh...eeeeee......eeeeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..............eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj1 B  34 VLEVKAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKN 297
                                ||  47        57        67        77        87        97 ||    112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
                               38|                                                      99|                                                                                                                                                                                                
                                43                                                      105                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4mj1c_ C: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee......................hhhhh..hhhhh...eeeeee....eeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..............eeeeeeeeeeeeee.....eeeee.eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj1 C  43 AITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSV 295
                                    52        62        72        82        92    || 112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292   
                                                                                 97|                                                                                                                                                                                           
                                                                                 108                                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains d4mj1d_ D: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeeee......................hhhhh..hhhhh...eeeeee...........eeeeeeeeeeeeee.hhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj1 D  32 VEVLEVKTGVDAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKN 297
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      


Chain E from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d4mj1e_ E: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeee......................hhhhh..hhhhh...eeeeee......eeeeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..............eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj1 E  32 VEVLEVKTGVITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKN 297
                                    41|       53        63        73        83        93     ||108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         
                                    41|                                                     99|                                                                                                                                                                                                
                                     44                                                     105
   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, 5)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MJ1)

(-) Gene Ontology  (10, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  VP1_POVBK | P03088
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q85235_POVBK | Q85235: 4mj0
        VP1_POVBK | P03088: 4mj0 5fua

(-) Related Entries Specified in the PDB File

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3bwr SV40 VP1 PENTAMER IN COMPLEX WITH GM1 OLIGOSACCHARIDE
3nxd JC POLYOMAVIRUS VP1 IN COMPLEX WITH LSTC
4mj0 BK POLYOMAVIRUS VP1 IN COMPLEX WITH GD3 OLIGOSACCHARIDE