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(-) Description

Title :  BK POLYOMAVIRUS VP1 PENTAMER IN COMPLEX WITH GD3 OLIGOSACCHARIDE
 
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 :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Antiparallel Beta Sandwich, Jelly-Roll Topology, Viral Protein, Polyomavirus, Receptor-Switching, Glycan Receptor, 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
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonBKPYV
    Organism ScientificBK POLYOMAVIRUS
    Organism Taxid10629

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric/Biological Unit (5, 23)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CL5Ligand/IonCHLORIDE ION
3GAL2Ligand/IonBETA-D-GALACTOSE
4GOL7Ligand/IonGLYCEROL
5SIA8Ligand/IonO-SIALIC ACID

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:62 , LEU A:67 , LYS A:68 , ASN A:272 , SER A:274 , THR A:276 , GLN A:278 , SIA A:402 , HOH A:574 , HOH A:596 , HOH A:619 , HOH A:684 , HOH A:697 , HOH B:590BINDING SITE FOR RESIDUE SIA A 401
02AC2SOFTWAREHIS A:150 , GLY A:222 , THR A:223 , HOH A:632 , HOH A:800BINDING SITE FOR RESIDUE GOL A 405
03AC3SOFTWARELYS A:180 , HIS A:193 , HOH A:795BINDING SITE FOR RESIDUE CL A 406
04AC4SOFTWARELEU B:62 , LEU B:67 , LYS B:68 , ASN B:272 , SER B:274 , THR B:276 , GLN B:278 , SIA B:402 , HOH B:542 , HOH B:548 , HOH B:640 , HOH B:677 , HOH B:723 , HOH C:540BINDING SITE FOR RESIDUE SIA B 401
05AC5SOFTWAREHIS A:138 , LYS B:68 , THR B:276 , SIA B:401BINDING SITE FOR RESIDUE SIA B 402
06AC6SOFTWAREGLU B:216 , ASN B:217 , ARG B:219 , ASP B:246 , VAL B:250 , GLY B:251 , PRO B:252 , HOH B:585 , HOH B:703BINDING SITE FOR RESIDUE GOL B 403
07AC7SOFTWAREHIS B:150 , PHE B:221 , GLY B:222 , THR B:223 , HOH B:570BINDING SITE FOR RESIDUE GOL B 404
08AC8SOFTWARELYS B:180 , HIS B:193BINDING SITE FOR RESIDUE CL B 405
09AC9SOFTWARELEU C:62 , LEU C:67 , LYS C:68 , ASN C:272 , SER C:274 , THR C:276 , GLN C:278 , SIA C:402 , HOH C:534 , HOH C:554 , HOH C:585 , HOH C:638 , HOH C:662 , HOH D:593BINDING SITE FOR RESIDUE SIA C 401
10BC1SOFTWAREHIS C:150 , PHE C:221 , GLY C:222 , THR C:223 , HOH C:536BINDING SITE FOR RESIDUE GOL C 404
11BC2SOFTWARELYS C:180 , HIS C:193BINDING SITE FOR RESIDUE CL C 405
12BC3SOFTWARELEU D:62 , LEU D:67 , LYS D:68 , ASN D:272 , SER D:274 , THR D:276 , GLN D:278 , SIA D:402 , HOH D:525 , HOH D:527 , HOH D:541 , HOH D:602 , HOH D:603 , HOH D:625 , HOH D:641BINDING SITE FOR RESIDUE SIA D 401
13BC4SOFTWAREGLY D:40 , ASP D:59 , SIA D:401 , HOH D:527 , HOH D:625 , HOH D:745 , HOH D:755 , HOH E:591BINDING SITE FOR RESIDUE SIA D 402
14BC5SOFTWAREHIS D:150 , PHE D:221 , GLY D:222 , THR D:223 , HOH D:709BINDING SITE FOR RESIDUE GOL D 403
15BC6SOFTWARELYS D:180 , HIS D:193BINDING SITE FOR RESIDUE CL D 404
16BC7SOFTWAREGLU E:216 , ASN E:217 , ARG E:219 , ASP E:246 , VAL E:250 , GLY E:251 , PRO E:252BINDING SITE FOR RESIDUE GOL E 401
17BC8SOFTWAREHIS E:150 , PHE E:221 , GLY E:222 , THR E:223 , HOH E:556 , HOH E:769BINDING SITE FOR RESIDUE GOL E 402
18BC9SOFTWARELYS E:180 , HIS E:193BINDING SITE FOR RESIDUE CL E 403
19CC1SOFTWAREVAL A:34 , LEU A:35 , GLU A:36 , VAL A:37 , THR A:39 , LYS A:68 , GLY A:249 , ARG A:293 , SIA A:401 , HOH A:566 , HOH A:627 , HOH A:655 , HOH A:702 , HOH A:729 , HOH A:747 , HOH A:775 , ASP B:74 , HIS E:138BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 402 TO 404
20CC2SOFTWAREHIS B:138 , LYS C:68 , THR C:276 , SIA C:401 , HOH C:662 , HOH C:669BINDING SITE FOR CHAIN C OF RESIDUES SIA C 402 AND GAL C 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MJ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MJ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4MJ0)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains d4mj0a_ A: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....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
                 4mj0 A  32 VEVLEVKTGVDAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVK 296
                                    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 B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4mj0b_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.eeeeeeeee......................hhhhh..hhhhh...eeeeee...........eeeeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj0 B  33 EVLEVKTDAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKN 297
                                  ||44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294   
                                 39|                                                                                                                                                                                                                                                               
                                  42                                                                                                                                                                                                                                                               

Chain C from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains d4mj0c_ C: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee......................hhhhh..hhhhh...eeeeee....eeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee.........ee...eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj0 C  34 VLEVITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSV 295
                               ||   49        59        69        79        89       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       
                              37|                                                   97|                                                                                                                                                                                            
                               44                                                   107                                                                                                                                                                                            

Chain D from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains d4mj0d_ D: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeeee......................hhhhh..hhhhh...eeeeee...........eeeeeeeeeeeeeeehhhhhhh....................eeeeeeee....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj0 D  32 VEVLEVKTGVDAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKNP 298
                                    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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4mj0e_ E: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....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
                 4mj0 E  32 VEVLEVKTGITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKNP 298
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294    
                                   40|                                                                                                                                                                                                                                                              
                                    44                                                                                                                                                                                                                                                              

   Legend:   → Mismatch (orange background)
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  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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MJ0)

(-) Gene Ontology  (10, 12)

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
        Q85235_POVBK | Q852354mj1
        VP1_POVBK | P030884mj1 5fua

(-) Related Entries Specified in the PDB File

3bwq STRUCTURE OF FREE SV40 VP1 PENTAMER
3bwr SV40 VP1 PENTAMER IN COMPLEX WITH GM1 OLIGOSACCHARIDE
3nxd JC POLYOMAVIRUS VP1 IN COMPLEX WITH LSTC
4mj1 BK POLYOMAVIRUS VP1 PENTAMER