3NXD - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   JC POLYOMAVIRUS VP1 IN COMPLEX WITH LSTC

Authors :   U. Neu, L. J. Stroeh, T. Stehle

Date :   13 Jul 10 (Deposition) - 17 Nov 10 (Release) - 17 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E  (1x)
Biol. Unit 2: A,B,C,D,E  (2x)

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

Reference :   U. Neu, M. S. Maginnis, A. S. Palma, L. J. Stroh, C. D. Nelson, T. Feizi, W. J. Atwood, T. Stehle
Structure-Function Analysis Of The Human Jc Polyomavirus Establishes The Lstc Pentasaccharide As A Functional Receptor Motif.
Cell Host Microbe V. 8 309 2010
PubMed-ID: 20951965 | Reference-DOI: 10.1016/J.CHOM.2010.09.004

Molecule 1 - MAJOR CAPSID PROTEIN VP1
	Chains	:	C, B, A, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 23-290
	Gene	:	VP1
	Organism Common	:	JCPYV
	Organism Scientific	:	JC POLYOMAVIRUS
	Organism Taxid	:	10632
	Strain	:	MAD-1
	Synonym	:	MAJOR STRUCTURAL PROTEIN VP1

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B	C	D	E
Biological Unit 2 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 21)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
4	GOL	5	Ligand/Ion	GLYCEROL
5	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	SIA	2	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (6, 21)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
4	GOL	5	Ligand/Ion	GLYCEROL
5	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	SIA	2	Ligand/Ion	O-SIALIC ACID

Biological Unit 2 (6, 42)

No.	Name	Count	Type	Full Name
1	BGC	4	Ligand/Ion	BETA-D-GLUCOSE
2	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
3	GAL	8	Ligand/Ion	BETA-D-GALACTOSE
4	GOL	10	Ligand/Ion	GLYCEROL
5	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	SIA	4	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GAL C:2 , NAG C:3 , 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:307 , HOH C:333 , HOH C:352 , HOH C:690 , HOH C:692 , PHE D:67	BINDING SITE FOR RESIDUE SIA C 1
02	AC2	SOFTWARE	GAL C:4 , HOH C:555	BINDING SITE FOR RESIDUE BGC C 5
03	AC3	SOFTWARE	NAG C:3 , BGC C:5 , ARG C:265 , HOH C:508 , HOH C:555 , HOH D:650	BINDING SITE FOR RESIDUE GAL C 4
04	AC4	SOFTWARE	SIA C:1 , GAL C:2 , GAL C:4 , ASN C:123 , SER C:266 , HOH C:333 , HOH C:417 , HOH C:508 , HOH C:959 , ASP D:65	BINDING SITE FOR RESIDUE NAG C 3
05	AC5	SOFTWARE	SIA C:1 , NAG C:3 , HOH C:651 , HOH C:718 , HOH C:802 , HOH C:857	BINDING SITE FOR RESIDUE GAL C 2
06	AC6	SOFTWARE	HIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , PRO C:72 , HOH C:486	BINDING SITE FOR RESIDUE GOL C 290
07	AC7	SOFTWARE	HIS C:142 , GLY C:214 , THR C:215	BINDING SITE FOR RESIDUE EDO C 291
08	AC8	SOFTWARE	GAL B:2 , NAG B:3 , LEU 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:292 , HOH B:312 , HOH B:338 , HOH B:955 , HOH B:1012 , HOH B:1019 , PHE C:67	BINDING SITE FOR RESIDUE SIA B 1
09	AC9	SOFTWARE	GAL B:4	BINDING SITE FOR RESIDUE BGC B 5
10	BC1	SOFTWARE	NAG B:3 , BGC B:5 , ARG B:265 , HOH B:385 , HOH B:732 , HOH C:620	BINDING SITE FOR RESIDUE GAL B 4
11	BC2	SOFTWARE	SIA B:1 , GAL B:2 , GAL B:4 , ASN B:123 , SER B:266 , HOH B:292 , HOH B:385 , HOH B:763 , HOH B:803 , ASP C:65	BINDING SITE FOR RESIDUE NAG B 3
12	BC3	SOFTWARE	SIA B:1 , NAG B:3 , HOH B:763 , HOH B:840 , GLU E:52	BINDING SITE FOR RESIDUE GAL B 2
13	BC4	SOFTWARE	HIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72	BINDING SITE FOR RESIDUE GOL B 290
14	BC5	SOFTWARE	SER A:62 , SER A:64 , SER A:69 , ASP A:70 , SER A:71 , PRO A:72 , HOH A:1009 , HIS E:121	BINDING SITE FOR RESIDUE GOL A 4
15	BC6	SOFTWARE	HIS A:142 , PHE A:144 , THR A:215 , HOH A:913	BINDING SITE FOR RESIDUE EDO A 5
16	BC7	SOFTWARE	HIS A:142 , LEU A:226 , HIS A:227	BINDING SITE FOR RESIDUE EDO A 6
17	BC8	SOFTWARE	HIS C:121 , SER D:62 , SER D:64 , SER D:69 , ASP D:70 , SER D:71 , PRO D:72 , HOH D:475	BINDING SITE FOR RESIDUE GOL D 2
18	BC9	SOFTWARE	HIS D:142 , PHE D:144 , GLY D:214 , THR D:215 , HOH D:549	BINDING SITE FOR RESIDUE EDO D 290
19	CC1	SOFTWARE	ARG A:265 , ASP B:65 , HIS D:121 , SER E:62 , SER E:64 , SER E:69 , ASP E:70 , SER E:71 , PRO E:72 , HOH E:741	BINDING SITE FOR RESIDUE GOL E 3
20	CC2	SOFTWARE	EDO E:4 , GLY E:214 , THR E:215	BINDING SITE FOR RESIDUE EDO E 290
21	CC3	SOFTWARE	THR E:234 , EDO E:290	BINDING SITE FOR RESIDUE EDO E 4

(no "SS Bond" information available for 3NXD)

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

Asymmetric Unit (11, 55)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_VP1_POVJC_001 *	D	66	H	VP1_POVJC	---	---	A/B/C/D/E	D	65	H
02	UniProt	VAR_VP1_POVJC_002 *	N	74	S	VP1_POVJC	---	---	A/B/C/D/E	N	73	S
03	UniProt	VAR_VP1_POVJC_003 *	R	75	K	VP1_POVJC	---	---	A/B/C/D/E	R	74	K
04	UniProt	VAR_VP1_POVJC_004 *	I	113	L	VP1_POVJC	---	---	A/B/C/D/E	I	112	L
05	UniProt	VAR_VP1_POVJC_005 *	S	117	T	VP1_POVJC	---	---	A/B/C/D/E	S	116	T
06	UniProt	VAR_VP1_POVJC_006 *	T	128	A	VP1_POVJC	---	---	A/B/C/D/E	T	127	A
07	UniProt	VAR_VP1_POVJC_007 *	L	158	V	VP1_POVJC	---	---	A/B/C/D/E	L	157	V
08	UniProt	VAR_VP1_POVJC_008 *	S	267	L	VP1_POVJC	---	---	A/B/C/D/E	S	266	L
09	UniProt	VAR_VP1_POVJC_009 *	S	269	F	VP1_POVJC	---	---	A/B/C/D/E	S	268	F
10	UniProt	VAR_VP1_POVJC_010 *	S	269	T	VP1_POVJC	---	---	A/B/C/D/E	S	268	T
11	UniProt	VAR_VP1_POVJC_011 *	S	269	Y	VP1_POVJC	---	---	A/B/C/D/E	S	268	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (11, 55)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_VP1_POVJC_001 *	D	66	H	VP1_POVJC	---	---	A/B/C/D/E	D	65	H
02	UniProt	VAR_VP1_POVJC_002 *	N	74	S	VP1_POVJC	---	---	A/B/C/D/E	N	73	S
03	UniProt	VAR_VP1_POVJC_003 *	R	75	K	VP1_POVJC	---	---	A/B/C/D/E	R	74	K
04	UniProt	VAR_VP1_POVJC_004 *	I	113	L	VP1_POVJC	---	---	A/B/C/D/E	I	112	L
05	UniProt	VAR_VP1_POVJC_005 *	S	117	T	VP1_POVJC	---	---	A/B/C/D/E	S	116	T
06	UniProt	VAR_VP1_POVJC_006 *	T	128	A	VP1_POVJC	---	---	A/B/C/D/E	T	127	A
07	UniProt	VAR_VP1_POVJC_007 *	L	158	V	VP1_POVJC	---	---	A/B/C/D/E	L	157	V
08	UniProt	VAR_VP1_POVJC_008 *	S	267	L	VP1_POVJC	---	---	A/B/C/D/E	S	266	L
09	UniProt	VAR_VP1_POVJC_009 *	S	269	F	VP1_POVJC	---	---	A/B/C/D/E	S	268	F
10	UniProt	VAR_VP1_POVJC_010 *	S	269	T	VP1_POVJC	---	---	A/B/C/D/E	S	268	T
11	UniProt	VAR_VP1_POVJC_011 *	S	269	Y	VP1_POVJC	---	---	A/B/C/D/E	S	268	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (11, 110)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_VP1_POVJC_001 *	D	66	H	VP1_POVJC	---	---	A/B/C/D/E	D	65	H
02	UniProt	VAR_VP1_POVJC_002 *	N	74	S	VP1_POVJC	---	---	A/B/C/D/E	N	73	S
03	UniProt	VAR_VP1_POVJC_003 *	R	75	K	VP1_POVJC	---	---	A/B/C/D/E	R	74	K
04	UniProt	VAR_VP1_POVJC_004 *	I	113	L	VP1_POVJC	---	---	A/B/C/D/E	I	112	L
05	UniProt	VAR_VP1_POVJC_005 *	S	117	T	VP1_POVJC	---	---	A/B/C/D/E	S	116	T
06	UniProt	VAR_VP1_POVJC_006 *	T	128	A	VP1_POVJC	---	---	A/B/C/D/E	T	127	A
07	UniProt	VAR_VP1_POVJC_007 *	L	158	V	VP1_POVJC	---	---	A/B/C/D/E	L	157	V
08	UniProt	VAR_VP1_POVJC_008 *	S	267	L	VP1_POVJC	---	---	A/B/C/D/E	S	266	L
09	UniProt	VAR_VP1_POVJC_009 *	S	269	F	VP1_POVJC	---	---	A/B/C/D/E	S	268	F
10	UniProt	VAR_VP1_POVJC_010 *	S	269	T	VP1_POVJC	---	---	A/B/C/D/E	S	268	T
11	UniProt	VAR_VP1_POVJC_011 *	S	269	Y	VP1_POVJC	---	---	A/B/C/D/E	S	268	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 3NXD)

Asymmetric 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:259
 aligned with VP1_POVJC | P03089 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:266
                                    34        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      
            VP1_POVJC    25 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 290
               SCOP domains d3nxda_ A: automated matches                                                                                                                                                                                                                                               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) (1) -----------------------------------------H-------SK-------------------------------------L---T----------A-----------------------------V------------------------------------------------------------------------------------------------------------L-F--------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------- SAPs(SNPs) (3)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nxd A  24 VEVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLN-------ILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 289
                                    33        43        53        63        73        83       | -     | 103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283      
                                                                                              91      99

Chain B from PDB  Type:PROTEIN  Length:258
 aligned with VP1_POVJC | P03089 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:265
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     
            VP1_POVJC    26 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 290
               SCOP domains d3nxdb_ B: automated matches                                                                                                                                                                                                                                              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) (1) ----------------------------------------H-------SK-------------------------------------L---T----------A-----------------------------V------------------------------------------------------------------------------------------------------------L-F--------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nxd B  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLN-------ILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 289
                                    34        44        54        64        74        84      |  -    |  104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284     
                                                                                             91      99

Chain C from PDB  Type:PROTEIN  Length:261
 aligned with VP1_POVJC | P03089 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:265
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     
            VP1_POVJC    26 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 290
               SCOP domains d3nxdc_ C: automated matches                                                                                                                                                                                                                                              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) (1) ----------------------------------------H-------SK-------------------------------------L---T----------A-----------------------------V------------------------------------------------------------------------------------------------------------L-F--------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nxd C  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDL----ILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 289
                                    34        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     
                                                                                                94   99

Chain D from PDB  Type:PROTEIN  Length:261
 aligned with VP1_POVJC | P03089 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:265
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     
            VP1_POVJC    26 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 290
               SCOP domains d3nxdd_ D: automated matches                                                                                                                                                                                                                                              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) (1) ----------------------------------------H-------SK-------------------------------------L---T----------A-----------------------------V------------------------------------------------------------------------------------------------------------L-F--------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nxd D  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDL----ILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 289
                                    34        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     
                                                                                                94   99

Chain E from PDB  Type:PROTEIN  Length:258
 aligned with VP1_POVJC | P03089 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:265
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     
            VP1_POVJC    26 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 290
               SCOP domains d3nxde_ E: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Polyoma_coat-3nxdE01 E:25-289                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) Polyoma_coat-3nxdE02 E:25-289                                                                                                                                                                                                                                             Pfam domains (2)
           Pfam domains (3) Polyoma_coat-3nxdE03 E:25-289                                                                                                                                                                                                                                             Pfam domains (3)
           Pfam domains (4) Polyoma_coat-3nxdE04 E:25-289                                                                                                                                                                                                                                             Pfam domains (4)
           Pfam domains (5) Polyoma_coat-3nxdE05 E:25-289                                                                                                                                                                                                                                             Pfam domains (5)
         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) (1) ----------------------------------------H-------SK-------------------------------------L---T----------A-----------------------------V------------------------------------------------------------------------------------------------------------L-F--------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nxd E  25 EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLN-------ILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQLRKRRVKN 289
                                    34        44        54        64        74        84      |  -    |  104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284     
                                                                                             91      99

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 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)

Jc polyomavirus [TaxId: 10632] (5)

1a	d3nxda_	A:
1b	d3nxdb_	B:
1c	d3nxdc_	C:
1d	d3nxdd_	D:
1e	d3nxde_	E:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Polyoma_coat (8)

JC polyomavirus (JCPyV) (JCV) (2)

1a	Polyoma_coat-3nxdE01	E:25-289
1b	Polyoma_coat-3nxdE02	E:25-289
1c	Polyoma_coat-3nxdE03	E:25-289
1d	Polyoma_coat-3nxdE04	E:25-289
1e	Polyoma_coat-3nxdE05	E:25-289

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (VP1_POVJC | P03089)

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:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	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.

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	Cis Peptide Bonds
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	3nxd
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	VP1_POVJC \| P03089
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	VP1_POVJC \| P03089
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UniProtKB/Swiss-Prot
	VP1_POVJC \| P03089	:	3nxg 4jcd 4jce 4jcf 4wdy 4wdz 4we0 4x14 4x15 4x16 4x17

1vps	HOMOLOGOUS PROTEIN POLYOMA VP1 IN COMPLEX WITH OLIGOSACCHARIDE
3bwr	HOMOLOGOUS PROTEIN SV40 VP1 IN COMPLEX WITH GM1
3nxg	JC POLYOMAVIRUS VP1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (11, 55)

PROSITE Motifs (0, 0)

Exons (0, 0)

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