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(-) Description

Title :  JC MAD-1 POLYOMAVIRUS VP1 IN COMPLEX WITH GD1A OLIGOSACCHARIDE
 
Authors :  L. J. Stroh, T. Stehle
Date :  24 Nov 14  (Deposition) - 22 Apr 15  (Release) - 27 May 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, Glycan, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Stroh, M. S. Maginnis, B. S. Blaum, C. D. Nelson, U. Neu, G. V. Gee, B. A. O'Hara, N. Motamedi, D. Dimaio, W. J. Atwood, T. Stehle
The Greater Affinity Of Jc Polyomavirus Capsid For Alpha 2, 6-Linked Lactoseries Tetrasaccharide C Than For Other Sialylated Glycans Is A Major Determinant Of Infectivity.
J. Virol. V. 89 6364 2015
PubMed-ID: 25855729  |  Reference-DOI: 10.1128/JVI.00489-15

(-) 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
    Fragment: UNP RESIDUES 23-290
    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  (4, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2GOL9Ligand/IonGLYCEROL
3K3Ligand/IonPOTASSIUM ION
4SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:62 , SER A:64 , SER A:69 , ASP A:70 , SER A:71 , PRO A:72 , MET A:76 , HOH A:533 , HIS E:121binding site for residue GOL A 301
02AC2SOFTWAREHIS A:142 , GLY A:214 , THR A:215binding site for residue EDO A 302
03AC3SOFTWAREGLU A:40 , HOH A:514 , THR B:205 , HOH B:438binding site for residue K A 303
04AC4SOFTWARELEU B:54 , LYS B:59 , SER B:60 , ASN B:123 , ASN B:264 , SER B:266 , SER B:268 , GLN B:270 , HOH B:427 , HOH B:488 , HOH B:489 , PHE C:67binding site for residue SIA B 301
05AC5SOFTWAREHIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72 , HOH B:406binding site for residue GOL B 302
06AC6SOFTWAREHIS B:142 , GLY B:214 , THR B:215 , EDO B:304 , GOL B:305 , HOH B:578binding site for residue EDO B 303
07AC7SOFTWAREHIS B:142 , HIS B:227 , EDO B:303 , GOL B:305 , HOH B:592binding site for residue EDO B 304
08AC8SOFTWAREHIS B:142 , PRO B:224 , VAL B:225 , EDO B:303 , EDO B:304 , HOH B:454 , HOH B:455 , HOH B:523 , HOH B:592binding site for residue GOL B 305
09AC9SOFTWAREGLU B:40 , THR C:205 , HOH C:550 , HOH C:551binding site for residue K B 306
10AD1SOFTWARELEU C:54 , LYS C:59 , SER C:60 , ASN C:123 , ASN C:264 , SER C:266 , SER C:268 , GLN C:270 , HOH C:445 , HOH C:448 , HOH C:449 , HOH C:472 , PHE D:67binding site for residue SIA C 301
11AD2SOFTWAREHIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , MET C:76 , HOH C:505binding site for residue GOL C 302
12AD3SOFTWAREHIS C:142 , GLY C:214 , THR C:215 , HOH C:548binding site for residue EDO C 303
13AD4SOFTWAREHIS C:142 , PRO C:224 , VAL C:225 , HOH C:414 , HOH C:440 , HOH C:537 , HOH C:608binding site for residue GOL C 304
14AD5SOFTWARELEU D:54 , LYS D:59 , SER D:60 , ASN D:123 , ASN D:264 , SER D:266 , SER D:268 , GLN D:270 , HOH D:436 , HOH D:588 , PHE E:67 , HOH E:616binding site for residue SIA D 301
15AD6SOFTWAREHIS C:121 , SER D:62 , SER D:64 , SER D:69 , ASP D:70 , SER D:71 , MET D:76 , HOH D:518 , HOH D:585binding site for residue GOL D 302
16AD7SOFTWAREHIS D:142 , GLY D:214 , THR D:215 , HOH D:484binding site for residue EDO D 303
17AD8SOFTWAREASP 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:401 , HOH E:407binding site for residue GOL E 301
18AD9SOFTWAREHIS E:142 , HIS E:227 , GOL E:303binding site for residue EDO E 302
19AE1SOFTWAREHIS E:142 , PRO E:224 , VAL E:225 , EDO E:302 , HOH E:427 , HOH E:442 , HOH E:480 , HOH E:534binding site for residue GOL E 303
20AE2SOFTWARESER A:62 , ILE A:63 , ALA E:126 , ASN E:130 , GLY E:131 , HOH E:511binding site for residue GOL E 304
21AE3SOFTWARETHR A:205 , HOH A:426 , HOH A:556 , HOH A:586 , GLU E:40 , HOH E:577binding site for residue K E 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X16)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X16)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X16)

(-) Exons   (0, 0)

(no "Exon" information available for 4X16)

(-) 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: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
                 4x16 A  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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 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
                 4x16 B  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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
                 4x16 C  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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...eeeee...................hhhhhh.....eeee......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x16 D  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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
                 4x16 E  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVK 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4X16)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X16)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X16)

(-) 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 4wdz 4we0 4x14 4x15 4x17

(-) Related Entries Specified in the PDB File

3nxd JC MAD-1 POLYOMAVIRUS VP1 IN COMPLEX WITH LSTC
3nxg UNLIGANDED JC MAD-1 POLYOMAVIRUS VP1