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(-) Description

Title :  JC MAD-1 POLYOMAVIRUS VP1 IN COMPLEX WITH GD1B 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 :  1.75
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, 31)

Asymmetric/Biological Unit (4, 31)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2GOL17Ligand/IonGLYCEROL
3K2Ligand/IonPOTASSIUM ION
4SIA5Ligand/IonO-SIALIC ACID

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:208 , ASN A:209 , ARG A:211 , ASP A:238 , GLY A:243 , PRO A:244binding site for residue GOL A 301
02AC2SOFTWAREHIS A:142 , PHE A:144 , GLY A:214 , THR A:215 , EDO A:303 , GOL A:304 , HOH A:593binding site for residue GOL A 302
03AC3SOFTWARETHR A:234 , GOL A:302binding site for residue EDO A 303
04AC4SOFTWAREHIS A:142 , PRO A:224 , VAL A:225 , GOL A:302 , HOH A:444 , HOH A:451 , HOH A:456binding site for residue GOL A 304
05AC5SOFTWARESER A:62 , SER A:64 , SER A:69 , ASP A:70 , SER A:71 , PRO A:72 , HOH A:441 , HIS E:121binding site for residue GOL A 305
06AC6SOFTWARETHR A:205 , HOH A:474 , HOH A:544 , HOH A:603 , GLU E:40 , HOH E:410binding site for residue K A 306
07AC7SOFTWARELEU 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:404 , HOH B:426 , HOH B:436 , PHE C:67binding site for residue SIA B 301
08AC8SOFTWAREHIS B:142 , GLY B:214 , THR B:215 , EDO B:303binding site for residue EDO B 302
09AC9SOFTWARETHR B:234 , EDO B:302binding site for residue EDO B 303
10AD1SOFTWAREHIS B:142 , PRO B:224 , VAL B:225 , HOH B:422 , HOH B:475 , HOH B:617binding site for residue GOL B 304
11AD2SOFTWAREHIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72 , HOH B:452binding site for residue GOL B 305
12AD3SOFTWAREHIS C:142 , LEU C:226 , HIS C:227 , GOL C:306 , GOL C:307binding site for residue EDO C 303
13AD4SOFTWAREGLU C:208 , ASN C:209 , ARG C:211 , ASP C:238 , GLY C:243 , PRO C:244binding site for residue GOL C 304
14AD5SOFTWARETHR C:234 , GOL C:306binding site for residue EDO C 305
15AD6SOFTWAREHIS C:142 , PHE C:144 , PHE C:213 , GLY C:214 , THR C:215 , EDO C:303 , EDO C:305 , GOL C:307 , HOH C:527binding site for residue GOL C 306
16AD7SOFTWAREPRO C:224 , VAL C:225 , EDO C:303 , GOL C:306 , HOH C:450 , HOH C:475 , HOH C:490 , HOH C:605binding site for residue GOL C 307
17AD8SOFTWAREHIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , MET C:76 , HOH C:410binding site for residue GOL C 308
18AD9SOFTWAREGLU D:208 , ASN D:209 , ARG D:211 , ASP D:238 , GLY D:243 , PRO D:244 , LEU D:245 , HOH D:440binding site for residue GOL D 303
19AE1SOFTWAREHIS D:142 , PHE D:144 , PHE D:213 , GLY D:214 , THR D:215 , EDO D:305 , HOH D:487 , HOH D:547binding site for residue GOL D 304
20AE2SOFTWARETHR D:234 , GOL D:304binding site for residue EDO D 305
21AE3SOFTWAREHIS C:121 , SER D:62 , SER D:64 , SER D:69 , ASP D:70 , SER D:71 , PRO D:72 , MET D:76 , HOH D:410binding site for residue GOL D 306
22AE4SOFTWAREGLU D:40 , HOH D:501 , THR E:205 , HOH E:498 , HOH E:594binding site for residue K D 307
23AE5SOFTWAREVAL E:82 , ALA E:83 , ARG E:84 , ASP E:190 , ASN E:192 , HOH E:554binding site for residue GOL E 301
24AE6SOFTWAREPHE E:213 , THR E:234 , GOL E:303binding site for residue EDO E 302
25AE7SOFTWAREHIS E:142 , PHE E:144 , GLY E:214 , THR E:215 , EDO E:302 , GOL E:304 , HOH E:581binding site for residue GOL E 303
26AE8SOFTWAREHIS E:142 , PRO E:224 , VAL E:225 , GOL E:303 , HOH E:429 , HOH E:484 , HOH E:494 , HOH E:616binding site for residue GOL E 304
27AE9SOFTWAREARG A:265 , ASP B:65 , THR B:66 , HIS D:121 , SER E:62 , SER E:64 , SER E:69 , ASP E:70 , SER E:71 , PRO E:72 , HOH E:454binding site for residue GOL E 305
28AF1SOFTWAREASN B:130 , LEU 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:425 , HOH C:427 , HOH C:439 , HOH C:446 , HOH C:541 , HOH C:569 , PHE D:67binding site for residues SIA C 301 and SIA C 302
29AF2SOFTWAREASN C:130 , LEU 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:403 , HOH D:425 , HOH D:475 , HOH D:530 , HOH D:560 , PHE E:67binding site for residues SIA D 301 and SIA D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X17)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X17)

(-) Exons   (0, 0)

(no "Exon" information available for 4X17)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4x17 A  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 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
                 4x17 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
                 4x17 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....eeee...................hhhhhh.....eee.......hhh.eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee.....eeeee.eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x17 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
                 4x17 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
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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 4X17)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X17)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X17)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  VP1_POVJC | P03089
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 Related Entries

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

UniProtKB/Swiss-Prot
        VP1_POVJC | P03089: 3nxd 3nxg 4jcd 4jce 4jcf 4wdy 4wdz 4we0 4x14 4x15 4x16

(-) Related Entries Specified in the PDB File

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