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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE POLYOMAVIRUS PTA STRAIN VP1 IN COMPLEX WITH THE GD1A GLYCAN
 
Authors :  A. M. Liaci, M. H. C. Buch, U. Neu, T. Stehle
Date :  21 Jul 15  (Deposition) - 28 Oct 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Murine Polyomavirus, Virus Protein, Carbohydrate Complex, Virus-Host Interaction, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Buch, A. M. Liaci, S. D. O'Hara, R. L. Garcea, U. Neu, T. Stehle
Structural And Functional Analysis Of Murine Polyomavirus Capsid Proteins Establish The Determinants Of Ligand Recognition And Pathogenicity.
Plos Pathog. V. 11 05104 2015
PubMed-ID: 26474293  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005104

(-) Compounds

Molecule 1 - 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
    Organism Scientific: MURINE POLYOMAVIRUS
    Organism Taxid: 10634
    Strain: PTA

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 29)

Asymmetric/Biological Unit (4, 29)
No.NameCountTypeFull Name
1GAL10Ligand/IonBETA-D-GALACTOSE
2GOL9Ligand/IonGLYCEROL
3NGA5Ligand/IonN-ACETYL-D-GALACTOSAMINE
4SIA5Ligand/IonO-SIALIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:200 , HOH A:528 , HOH A:538 , THR D:147 , VAL D:148binding site for residue GOL A 401
02AC2SOFTWAREGLU A:235 , ASN A:236 , ARG A:238 , ASP A:265 , GLY A:270 , HOH A:647binding site for residue GOL A 406
03AC3SOFTWARELYS B:186 , GLU B:187 , GLU B:188 , HOH B:654binding site for residue GOL B 401
04AC4SOFTWAREGLU B:235 , ASN B:236 , ARG B:238 , ASP B:265 , GLY B:270 , LEU B:272 , HOH B:626binding site for residue GOL B 406
05AC5SOFTWAREGLU C:235 , ASN C:236 , ARG C:238 , ASP C:265 , VAL C:269 , GLY C:270 , LEU C:272binding site for residue GOL C 405
06AC6SOFTWARETHR D:67 , GLU D:68 , GLY D:69 , GLN D:71 , ARG D:77 , HOH D:546binding site for residue GOL D 401
07AC7SOFTWARELYS D:186 , GLU D:187 , GLU D:188 , HOH D:789binding site for residue GOL D 406
08AC8SOFTWAREGLU D:235 , ASN D:236 , ARG D:238 , ASP D:265 , GLY D:270binding site for residue GOL D 407
09AC9SOFTWAREGLU E:235 , ASN E:236 , ARG E:238 , ASP E:265 , GLY E:270 , LEU E:272 , HOH E:694binding site for residue GOL E 405
10AD1SOFTWARETYR A:72 , ARG A:77 , GLY A:78 , GLU A:91 , ASN A:93 , THR A:94 , THR A:291 , ASN A:293 , HIS A:298 , HOH A:548 , HOH A:550 , HOH A:557 , HOH A:567 , HOH A:570 , HOH A:599 , HOH A:610 , HOH A:616 , HOH A:648 , HOH A:660 , HOH A:668 , HOH A:678 , HOH A:710 , HOH A:728 , HOH A:730 , ASP B:85 , TYR E:294binding site for Poly-Saccharide residues SIA A 402 through GAL A 405
11AD2SOFTWARETYR A:72 , ARG A:77 , GLY A:78 , GLU A:91 , ASN A:93 , THR A:94 , THR A:291 , ASN A:293 , HIS A:298 , HOH A:548 , HOH A:550 , HOH A:557 , HOH A:567 , HOH A:570 , HOH A:599 , HOH A:610 , HOH A:616 , HOH A:648 , HOH A:660 , HOH A:668 , HOH A:678 , HOH A:710 , HOH A:728 , HOH A:730 , TYR B:72 , ARG B:77 , GLY B:78 , ASP B:85 , GLU B:91 , ASN B:93 , THR B:94 , THR B:291 , ASN B:293 , HIS B:298 , HOH B:507 , HOH B:530 , HOH B:580 , HOH B:600 , HOH B:605 , HOH B:608 , HOH B:646 , HOH B:657 , HOH B:683 , HOH B:695 , HOH B:698 , HOH B:742 , ASP C:85 , TYR E:294binding site for Poly-Saccharide residues SIA B 402 through GAL B 405
12AD3SOFTWARETYR B:72 , ARG B:77 , GLY B:78 , GLU B:91 , ASN B:93 , THR B:94 , LYS B:186 , GLU B:187 , GLU B:188 , THR B:291 , ASN B:293 , HIS B:298 , HOH B:507 , HOH B:530 , HOH B:580 , HOH B:600 , HOH B:605 , HOH B:608 , HOH B:646 , HOH B:654 , HOH B:657 , HOH B:683 , HOH B:695 , HOH B:698 , HOH B:742 , TYR C:72 , ARG C:77 , GLY C:78 , ASP C:85 , GLU C:91 , ASN C:93 , THR C:94 , GLU C:235 , ASN C:236 , ARG C:238 , ASP C:265 , VAL C:269 , GLY C:270 , LEU C:272 , THR C:291 , ASN C:293 , HIS C:298 , HOH C:511 , HOH C:515 , HOH C:552 , HOH C:563 , HOH C:596 , HOH C:634 , HOH C:646 , HOH C:691 , HOH C:694 , HOH C:698 , HOH C:729 , ASP D:85binding site for Poly-Saccharide residues SIA C 401 through GAL C 404
13AD4SOFTWAREGLY C:78 , GLU C:91 , ASN C:93 , THR C:94 , GLU C:235 , ASN C:236 , ARG C:238 , ASP C:265 , VAL C:269 , GLY C:270 , LEU C:272 , SIA C:401 , HOH C:511 , HOH C:552 , HOH C:634 , HOH C:646 , HOH C:691 , HOH C:698 , TYR D:72 , ARG D:77 , GLY D:78 , GLU D:91 , ASN D:93 , THR D:94 , THR D:291 , ASN D:293 , HIS D:298 , HOH D:511 , HOH D:534 , HOH D:546 , HOH D:584 , HOH D:617 , HOH D:620 , HOH D:673 , HOH D:676 , HOH D:694 , HOH D:719 , HOH D:722 , HOH D:728 , HOH D:742 , ASP E:85binding site for Poly-Saccharide residues SIA D 402 through GAL D 405
14AD5SOFTWAREASP A:85 , THR D:67 , GLU D:68 , GLY D:69 , GLN D:71 , TYR D:72 , ARG D:77 , GLY D:78 , GLU D:91 , ASN D:93 , THR D:94 , THR D:291 , ASN D:293 , HIS D:298 , HOH D:511 , HOH D:534 , HOH D:546 , HOH D:584 , HOH D:617 , HOH D:620 , HOH D:673 , HOH D:676 , HOH D:694 , HOH D:719 , HOH D:722 , HOH D:728 , HOH D:742 , TYR E:72 , ARG E:77 , GLY E:78 , ASP E:85 , GLU E:91 , ASN E:93 , THR E:94 , GLU E:235 , ASN E:236 , ARG E:238 , ASP E:265 , GLY E:270 , LEU E:272 , THR E:291 , ASN E:293 , HIS E:298 , HOH E:516 , HOH E:528 , HOH E:572 , HOH E:573 , HOH E:581 , HOH E:620 , HOH E:648 , HOH E:650 , HOH E:678 , HOH E:690 , HOH E:694 , HOH E:699 , HOH E:713 , HOH E:778binding site for Poly-Saccharide residues SIA E 401 through GAL E 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CPY)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr A:62 -Pro A:63
2Thr B:62 -Pro B:63
3Thr C:62 -Pro C:63
4Thr D:62 -Pro D:63
5Thr E:62 -Pro E:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CPY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CPY)

(-) Exons   (0, 0)

(no "Exon" information available for 5CPY)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeeeeee...............hhhhh.................hhhhh...eeeeee......eeeeeeeeeeeee.hhhhhhh......eee....eeee......eeeeeeee....eeee...............hhhhhhh...hhhhhh.....eee...........eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee......eeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpy A  33 GMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPENNTLPTWSMAKLQLPMLNTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    42        52        62        72        82        92       102      |118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
                                                                                                      109|                                                                                                                                                                                                        
                                                                                                       116                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeeeeee...............hhhhh.................hhhhh...eeeeee......eeeeeeeeeeeee.hhhhhhh......eee....eeee......eeeeeeee....eeee...............hhhhhhh...hhhhhh.....eee...........eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee......eeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpy B  33 GMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPENNTLPTWSMAKLQLPMLNTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    42        52        62        72        82        92       102      |118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
                                                                                                      109|                                                                                                                                                                                                        
                                                                                                       116                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeeeeee...............hhhhh.................hhhhh...eeeeee......eeeeeeeeeeeee.hhhhhhh......eee....eeee......eeeeeeee....eeee...............hhhhhhh...hhhhhh.....eee...........eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee......eeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpy C  33 GMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPENNTLPTWSMAKLQLPMLNTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    42        52        62        72        82        92       102      |118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
                                                                                                      109|                                                                                                                                                                                                        
                                                                                                       116                                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeeeeeee...............hhhhh.................hhhhh...eeeeee............eeeeeeeeeeeee.hhhhhhh......eee....eeee......eeeeeeee....eeee...............hhhhhhh...hhhhhh.....eee...........eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee......eeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpy D  34 MEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPENNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313   


Chain E from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeeeeee...............hhhhh.................hhhhh...eeeeee......eeeeeeeeeeeee.hhhhhhh......eee....eeee......eeeeeeee....eeee...............hhhhhhh...hhhhhh.....eee...........eee.......eeeeeeee.......eeeee....ee..........hhh.eeeeeeeeeeeeee......eeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpy E  33 GMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPENNTLPTWSMAKLQLPMLNTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    42        52        62        72        82        92       102      |118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
                                                                                                      109|                                                                                                                                                                                                        
                                                                                                       116
   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 5CPY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CPY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CPY)

(-) Gene Ontology  (10, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  VP1_POVMP | P49302
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q85068_POVM3 | Q85068: 5cpu 5cpw 5cpx
        VP1_POVMP | P49302: 1cn3 1sid 1sie 1vpn 1vps 5cpu 5cpw 5cpx 5cpz 5cq0

(-) Related Entries Specified in the PDB File

1vpn 1VPN CONTAINS THE VP1 PROTEIN OF THE RA STRAIN WITHOUT ANY COMPLEXED GLYCANS.
1vps 1VPS CONTAINS THE VP1 PROTEIN OF THE RA STRAIN COMPLEXED WITH A DIFFERENT GLYCAN.