3S7X - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   UNASSEMBLED WASHINGTON UNIVERSITY POLYOMAVIRUS VP1 PENTAMER R198K MUTANT

Authors :   U. Neu, J. Wang, T. Stehle

Date :   27 May 11 (Deposition) - 29 Jun 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Jelly-Roll Fold, Antiparallel Beta Sandwich, Major Capsid Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Neu, J. Wang, D. Macejak, R. L. Garcea, T. Stehle
Structures Of The Major Capsid Proteins Of The Human Ki And Wu Polyomaviruses.
J. Virol. V. 85 7384 2011
PubMed-ID: 21543504 | Reference-DOI: 10.1128/JVI.00382-11

Molecule 1 - MAJOR CAPSID PROTEIN VP1
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 34-296
	Gene	:	VP1
	Mutation	:	YES
	Organism Scientific	:	WU POLYOMAVIRUS
	Organism Taxid	:	440266
	Synonym	:	MAJOR STRUCTURAL PROTEIN VP1

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION
2	GOL	5	Ligand/Ion	GLYCEROL
3	NA	5	Ligand/Ion	SODIUM ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:138 , LYS A:274 , ASN A:275	BINDING SITE FOR RESIDUE GOL A 1
02	AC2	SOFTWARE	LEU B:137 , THR B:138 , LYS B:274	BINDING SITE FOR RESIDUE GOL B 1
03	AC3	SOFTWARE	LEU C:137 , THR C:138 , LYS C:274	BINDING SITE FOR RESIDUE GOL C 1
04	AC4	SOFTWARE	LEU D:137 , THR D:138 , LYS D:274	BINDING SITE FOR RESIDUE GOL D 1
05	AC5	SOFTWARE	LEU E:137 , THR E:138 , LYS E:274	BINDING SITE FOR RESIDUE GOL E 1
06	AC6	SOFTWARE	LYS B:57 , SER C:193	BINDING SITE FOR RESIDUE CL B 297
07	AC7	SOFTWARE	SER A:193 , LYS E:57	BINDING SITE FOR RESIDUE CL A 297
08	AC8	SOFTWARE	LYS A:57	BINDING SITE FOR RESIDUE CL A 298
09	AC9	SOFTWARE	SER D:193	BINDING SITE FOR RESIDUE CL D 297
10	BC1	SOFTWARE	LYS D:57 , SER E:193	BINDING SITE FOR RESIDUE CL D 298
11	BC2	SOFTWARE	GLU E:125 , SER E:240	BINDING SITE FOR RESIDUE NA E 297
12	BC3	SOFTWARE	GLU A:125 , SER A:240	BINDING SITE FOR RESIDUE NA A 299
13	BC4	SOFTWARE	SER B:240	BINDING SITE FOR RESIDUE NA B 298
14	BC5	SOFTWARE	GLU C:125 , SER C:240	BINDING SITE FOR RESIDUE NA C 297
15	BC6	SOFTWARE	GLU D:125 , SER D:240	BINDING SITE FOR RESIDUE NA D 299

Asymmetric/Biological Unit

No.	Residues
1	A:112	-	B:112
2	C:112	-	E:112
3	D:112	-	D:112

(no "Cis Peptide Bond" information available for 3S7X)

(no "SAP(SNP)/Variant" information available for 3S7X)

(no "PROSITE Motif" information available for 3S7X)

(no "Exon" information available for 3S7X)

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:263
 aligned with VP1_POVWU | A5HBD5 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:266
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      
            VP1_POVWU    31 VRKGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPRARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 296
               SCOP domains d3s7xa_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee........eeeeeee..ee..................hhhhhh...hhhh.ee.eeeee.......---..eeeeeeeeeeeeeee....hhhhh............eeeeeeee....eeee.................................eee..........eee.......eeeeeeee.......eeeee....ee........ee.....eeeeeeeeeee....eee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s7x A  31 SHMGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPN---ECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 296
                                    40        50        60        70        80        90       100      |  -|      120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      
                                                                                                      107 111

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with VP1_POVWU | A5HBD5 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:265
                                    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     
            VP1_POVWU    32 RKGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPRARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 296
               SCOP domains d3s7xb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee........eeeeeee..ee..................hhhhhh...hhhh.ee.eeeee......----..eeeeeeeeeeeeeee....hhhhh............eeeeeeee....eeee.................................eee..........eee.......eeeeeeee.......eeeee....ee........ee.....eeeeeeeeeee....eee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s7x B  32 HMGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIP----ECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 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     
                                                                                                    106  111

Chain C from PDB  Type:PROTEIN  Length:263
 aligned with VP1_POVWU | A5HBD5 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:266
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      
            VP1_POVWU    31 VRKGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPRARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 296
               SCOP domains d3s7xc_ C: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee........eeeeeee..ee..................hhhhhh...hhhh.ee.eeeee.......---..eeeeeeeeeeeeeee.....................eeeeeeee....eeee.................................eee..........eee.......eeeeeeee.......eeeee....ee........ee.....eeeeeeeeeee....eee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s7x C  31 SHMGGVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPN---ECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 296
                                    40        50        60        70        80        90       100      |  -|      120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      
                                                                                                      107 111

Chain D from PDB  Type:PROTEIN  Length:260
 aligned with VP1_POVWU | A5HBD5 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:262
                                    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  
            VP1_POVWU    35 GVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPRARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 296
               SCOP domains d3s7xd_ D: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeeeee..ee..................hhhhhh...hhhh.ee.eeeee.......--...eeeeeeeeeeeeeee....hhhhh............eeeeeeee....eeee.................................eee..........eee.......eeeeeeee.......eeeee....ee........ee.....eeeeeeeeeee....eee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s7x D  35 GVDVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPN--SECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRVRN 296
                                    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  
                                                                                                  107  |                                                                                                                                                                                          
                                                                                                     110

Chain E from PDB  Type:PROTEIN  Length:254
 aligned with VP1_POVWU | A5HBD5 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:258
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286        
            VP1_POVWU    37 DVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIPNQVSECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPRARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRV 294
               SCOP domains d3s7xe_ E: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Polyoma_coat-3s7xE01 E:37-294                                                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) Polyoma_coat-3s7xE02 E:37-294                                                                                                                                                                                                                                      Pfam domains (2)
           Pfam domains (3) Polyoma_coat-3s7xE03 E:37-294                                                                                                                                                                                                                                      Pfam domains (3)
           Pfam domains (4) Polyoma_coat-3s7xE04 E:37-294                                                                                                                                                                                                                                      Pfam domains (4)
           Pfam domains (5) Polyoma_coat-3s7xE05 E:37-294                                                                                                                                                                                                                                      Pfam domains (5)
         Sec.struct. author .............eeeeeee..ee..................hhhhhh...hhhh.ee.eeeee......----...eeeeeeeeeeeeee....hhhhh............eeeeeeee....eeee.................................eee..........eee.......eeeeeeee.......eeeee....ee........ee.....eeeeeeeeeee....eee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s7x E  37 DVLAAVPLSEETEFKVELFVKPVIGNAEGTTPHYWSISSPLKTAEAANVTPDADTTVCYSLSQVAPPDIP----ECDMLIWELYRMETEVLVLPVLNAGILTTGGVGGIAGPQLYFWAVGGQPLDVLGLAPTEKYKGPAQYTVNPKTNGTVPHVYSSSETPKARVTNEKYSIESWVADPSRNDNCRYFGRMVGGAATPPVVSFSNNSTIPLLDENGIGILCLQGRLYITCADLLGVNKNRVHTGLSRFFRLHFRQRRV 294
                                    46        56        66        76        86        96       106    |  116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286        
                                                                                               106  111

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) (278)

Superfamily: Group I dsDNA viruses (30)

Family: automated matches (11)

Protein domain: automated matches (11)

Wu polyomavirus [TaxId: 440266] (1)

1a	d3s7xa_	A:
1b	d3s7xb_	B:
1c	d3s7xc_	C:
1d	d3s7xd_	D:
1e	d3s7xe_	E:

(no "CATH Domain" information available for 3S7X)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Polyoma_coat] (8)

Family: Polyoma_coat (8)

WU polyomavirus (WUPyV) (1)

1a	Polyoma_coat-3s7xE01	E:37-294
1b	Polyoma_coat-3s7xE02	E:37-294
1c	Polyoma_coat-3s7xE03	E:37-294
1d	Polyoma_coat-3s7xE04	E:37-294
1e	Polyoma_coat-3s7xE05	E:37-294

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E (VP1_POVWU | A5HBD5)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0039620	T=7 icosahedral viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=7 symmetry. The T=7 capsid is composed of 12 pentameric and 60 hexameric capsomeres.
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3s7x)

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	3s7x
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1vps	OTHER POLYOMAVIRUS VP1 CAPSOMER
3bwr	OTHER POLYOMAVIRUS VP1 CAPSOMER
3nxg	OTHER POLYOMAVIRUS VP1 CAPSOMER
3s7v	RELATED POLYOMAVIRUS VP1 CAPSOMER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 5)

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Pfam Domains (1, 5)

Gene Ontology (9, 9)

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