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3NXD
Biol. Unit 1
Info
Asym.Unit (236 KB)
Biol.Unit 1 (228 KB)
Biol.Unit 2 (453 KB)
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(1)
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
[
close entry info
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Hetero Components
(6, 21)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
3d: BETA-D-GALACTOSE (GALd)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6a: O-SIALIC ACID (SIAa)
6b: O-SIALIC ACID (SIAb)
View:
Select:
Label:
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
[
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]
Sites
(21, 21)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
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
[
close Site info
]
SAPs(SNPs)/Variants
(11, 55)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_VP1_POVJC_001 (D65H, chain A/B/C/D/E, )
02: VAR_VP1_POVJC_002 (N73S, chain A/B/C/D/E, )
03: VAR_VP1_POVJC_003 (R74K, chain A/B/C/D/E, )
04: VAR_VP1_POVJC_004 (I112L, chain A/B/C/D/E, )
05: VAR_VP1_POVJC_005 (S116T, chain A/B/C/D/E, )
06: VAR_VP1_POVJC_006 (T127A, chain A/B/C/D/E, )
07: VAR_VP1_POVJC_007 (L157V, chain A/B/C/D/E, )
08: VAR_VP1_POVJC_008 (S266L, chain A/B/C/D/E, )
09: VAR_VP1_POVJC_009 (S268F, chain A/B/C/D/E, )
10: VAR_VP1_POVJC_010 (S268T, chain A/B/C/D/E, )
11: VAR_VP1_POVJC_011 (S268Y, chain A/B/C/D/E, )
View:
Select:
Label:
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)
[
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]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d3nxda_ (A:)
1b: SCOP_d3nxdb_ (B:)
1c: SCOP_d3nxdc_ (C:)
1d: SCOP_d3nxdd_ (D:)
1e: SCOP_d3nxde_ (E:)
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Protein Domains
(
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(
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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:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Polyoma_coat_3nxdE01 (E:25-289)
1b: PFAM_Polyoma_coat_3nxdE02 (E:25-289)
1c: PFAM_Polyoma_coat_3nxdE03 (E:25-289)
1d: PFAM_Polyoma_coat_3nxdE04 (E:25-289)
1e: PFAM_Polyoma_coat_3nxdE05 (E:25-289)
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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
[
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]
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