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3GZT
Biol. Unit 1
Info
Asym.Unit (506 KB)
Biol.Unit 1, α-C (28.7 MB)
Biol.Unit 1 (28.7 MB)
(using Jmol or JSmol)
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(1)
Title
:
VP7 RECOATED ROTAVIRUS DLP
Authors
:
J. Z. Chen, E. C. Settembre, S. C. Harrison, N. Grigorieff
Date
:
07 Apr 09 (Deposition) - 14 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
3.80
Chains
:
Asym. Unit : B,F,G,H,I,J,K,L,M,N,O,P,Q,X
#
Biol. Unit 1: B,F,G,H,I,J,K,L,M,N,O,P,Q,X
#
(60x)
(
#
: chains that contain no standard or modified protein/DNA/RNA residue)
Keywords
:
Rotavirus, Vp7, Vp6, Vp2, 7Rp, Dlp, Icosahedral Virus, Capsid Protein, Disulfide Bond, Endoplasmic Reticulum, Glycoprotein, Membrane, Transmembrane, Virion, Virus
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Z. Chen, E. C. Settembre, S. T. Aoki, X. Zhang, A. R. Bellamy, P. R. Dormitzer, S. C. Harrison, N. Grigorieff
Molecular Interactions In Rotavirus Assembly And Uncoating Seen By High-Resolution Cryo-Em
Proc. Natl. Acad. Sci. Usa V. 106 10644 2009
[
close entry info
]
Hetero Components
(1, 1560)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1aa: CALCIUM ION (CAaa)
1ab: CALCIUM ION (CAab)
1ac: CALCIUM ION (CAac)
1ad: CALCIUM ION (CAad)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
1q: CALCIUM ION (CAq)
1r: CALCIUM ION (CAr)
1s: CALCIUM ION (CAs)
1t: CALCIUM ION (CAt)
1u: CALCIUM ION (CAu)
1v: CALCIUM ION (CAv)
1w: CALCIUM ION (CAw)
1x: CALCIUM ION (CAx)
1y: CALCIUM ION (CAy)
1z: CALCIUM ION (CAz)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
2m: N-ACETYL-D-GLUCOSAMINE (NAGm)
2n: N-ACETYL-D-GLUCOSAMINE (NAGn)
2o: N-ACETYL-D-GLUCOSAMINE (NAGo)
2p: N-ACETYL-D-GLUCOSAMINE (NAGp)
2q: N-ACETYL-D-GLUCOSAMINE (NAGq)
2r: N-ACETYL-D-GLUCOSAMINE (NAGr)
2s: N-ACETYL-D-GLUCOSAMINE (NAGs)
2t: N-ACETYL-D-GLUCOSAMINE (NAGt)
2u: N-ACETYL-D-GLUCOSAMINE (NAGu)
2v: N-ACETYL-D-GLUCOSAMINE (NAGv)
2w: N-ACETYL-D-GLUCOSAMINE (NAGw)
2x: N-ACETYL-D-GLUCOSAMINE (NAGx)
2y: N-ACETYL-D-GLUCOSAMINE (NAGy)
2z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
NAG
1560
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(54, 54)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAG B:2 , ASN B:69
BINDING SITE FOR RESIDUE NAG B 1
02
AC2
SOFTWARE
NAG B:1
BINDING SITE FOR RESIDUE NAG B 2
03
AC3
SOFTWARE
NAG G:8 , ASN G:69
BINDING SITE FOR RESIDUE NAG G 7
04
AC4
SOFTWARE
NAG G:7
BINDING SITE FOR RESIDUE NAG G 8
05
AC5
SOFTWARE
NAG H:10 , ASN H:69
BINDING SITE FOR RESIDUE NAG H 9
06
AC6
SOFTWARE
NAG H:9
BINDING SITE FOR RESIDUE NAG H 10
07
AC7
SOFTWARE
NAG F:12 , ASN F:69
BINDING SITE FOR RESIDUE NAG F 11
08
AC8
SOFTWARE
NAG F:11
BINDING SITE FOR RESIDUE NAG F 12
09
AC9
SOFTWARE
NAG J:14 , ASN J:69
BINDING SITE FOR RESIDUE NAG J 13
10
BC1
SOFTWARE
NAG J:13
BINDING SITE FOR RESIDUE NAG J 14
11
BC2
SOFTWARE
NAG K:16 , ASN K:69
BINDING SITE FOR RESIDUE NAG K 15
12
BC3
SOFTWARE
NAG K:15
BINDING SITE FOR RESIDUE NAG K 16
13
BC4
SOFTWARE
NAG I:18 , ASN I:69
BINDING SITE FOR RESIDUE NAG I 17
14
BC5
SOFTWARE
NAG I:17
BINDING SITE FOR RESIDUE NAG I 18
15
BC6
SOFTWARE
NAG M:20 , ASN M:69
BINDING SITE FOR RESIDUE NAG M 19
16
BC7
SOFTWARE
NAG M:19
BINDING SITE FOR RESIDUE NAG M 20
17
BC8
SOFTWARE
NAG N:22 , ASN N:69
BINDING SITE FOR RESIDUE NAG N 21
18
BC9
SOFTWARE
NAG N:21
BINDING SITE FOR RESIDUE NAG N 22
19
CC1
SOFTWARE
NAG L:24 , ASN L:69
BINDING SITE FOR RESIDUE NAG L 23
20
CC2
SOFTWARE
NAG L:23
BINDING SITE FOR RESIDUE NAG L 24
21
CC3
SOFTWARE
NAG P:26 , ASN P:69
BINDING SITE FOR RESIDUE NAG P 25
22
CC4
SOFTWARE
NAG P:25
BINDING SITE FOR RESIDUE NAG P 26
23
CC5
SOFTWARE
NAG Q:28 , ASN Q:69
BINDING SITE FOR RESIDUE NAG Q 27
24
CC6
SOFTWARE
NAG Q:27
BINDING SITE FOR RESIDUE NAG Q 28
25
CC7
SOFTWARE
NAG O:30 , ASN O:69
BINDING SITE FOR RESIDUE NAG O 29
26
CC8
SOFTWARE
NAG O:29
BINDING SITE FOR RESIDUE NAG O 30
27
CC9
SOFTWARE
ASP B:301
BINDING SITE FOR RESIDUE CA B 320
28
DC1
SOFTWARE
ASP B:95
BINDING SITE FOR RESIDUE CA B 321
29
DC2
SOFTWARE
GLN B:177 , ASP B:179 , ASP B:228 , VAL B:229 , ASP B:231
BINDING SITE FOR RESIDUE CA B 322
30
DC3
SOFTWARE
GLY B:206 , THR B:214 , PHE B:215 , GLU B:216
BINDING SITE FOR RESIDUE CA B 323
31
DC4
SOFTWARE
ASP F:301 , GLN H:177 , ASP H:179 , ASP H:228 , VAL H:229 , ASP H:231
BINDING SITE FOR RESIDUE CA H 324
32
DC5
SOFTWARE
ASP F:95 , GLY H:206 , THR H:214 , PHE H:215 , GLU H:216
BINDING SITE FOR RESIDUE CA H 325
33
DC6
SOFTWARE
GLN F:177 , ASP F:179 , ASP F:228 , VAL F:229 , ASP F:231 , ASP G:301
BINDING SITE FOR RESIDUE CA F 326
34
DC7
SOFTWARE
GLY F:206 , THR F:214 , PHE F:215 , GLU F:216 , ASP G:95
BINDING SITE FOR RESIDUE CA F 327
35
DC8
SOFTWARE
GLN G:177 , ASP G:179 , ASP G:228 , VAL G:229 , ASP G:231 , ASP H:301
BINDING SITE FOR RESIDUE CA G 328
36
DC9
SOFTWARE
GLY G:206 , THR G:214 , PHE G:215 , GLU G:216 , ASP H:95
BINDING SITE FOR RESIDUE CA G 329
37
EC1
SOFTWARE
ASP I:301 , GLN K:177 , ASP K:179 , ASP K:228 , VAL K:229 , ASP K:231
BINDING SITE FOR RESIDUE CA K 330
38
EC2
SOFTWARE
ASP I:95 , GLY K:206 , THR K:214 , PHE K:215 , GLU K:216
BINDING SITE FOR RESIDUE CA K 331
39
EC3
SOFTWARE
GLN I:177 , ASP I:179 , ASP I:228 , VAL I:229 , ASP I:231 , ASP J:301
BINDING SITE FOR RESIDUE CA I 332
40
EC4
SOFTWARE
GLY I:206 , THR I:214 , PHE I:215 , GLU I:216 , ASP J:95
BINDING SITE FOR RESIDUE CA I 333
41
EC5
SOFTWARE
GLN J:177 , ASP J:179 , ASP J:228 , VAL J:229 , ASP J:231 , ASP K:301
BINDING SITE FOR RESIDUE CA J 334
42
EC6
SOFTWARE
GLY J:206 , THR J:214 , PHE J:215 , GLU J:216 , ASP K:95
BINDING SITE FOR RESIDUE CA J 335
43
EC7
SOFTWARE
ASP L:301 , GLN N:177 , ASP N:179 , ASP N:228 , VAL N:229 , ASP N:231
BINDING SITE FOR RESIDUE CA N 336
44
EC8
SOFTWARE
ASP L:95 , GLY N:206 , THR N:214 , PHE N:215 , GLU N:216
BINDING SITE FOR RESIDUE CA N 337
45
EC9
SOFTWARE
GLN L:177 , ASP L:179 , ASP L:228 , VAL L:229 , ASP L:231 , ASP M:301
BINDING SITE FOR RESIDUE CA L 338
46
FC1
SOFTWARE
GLY L:206 , THR L:214 , PHE L:215 , GLU L:216 , ASP M:95
BINDING SITE FOR RESIDUE CA L 339
47
FC2
SOFTWARE
GLN M:177 , ASP M:179 , ASP M:228 , VAL M:229 , ASP M:231 , ASP N:301
BINDING SITE FOR RESIDUE CA M 340
48
FC3
SOFTWARE
GLY M:206 , THR M:214 , PHE M:215 , GLU M:216 , ASP N:95
BINDING SITE FOR RESIDUE CA M 341
49
FC4
SOFTWARE
ASP O:301 , GLN Q:177 , ASP Q:179 , ASP Q:228 , VAL Q:229 , ASP Q:231
BINDING SITE FOR RESIDUE CA Q 342
50
FC5
SOFTWARE
ASP O:95 , GLY Q:206 , THR Q:214 , PHE Q:215 , GLU Q:216
BINDING SITE FOR RESIDUE CA Q 343
51
FC6
SOFTWARE
GLN O:177 , ASP O:179 , ASP O:228 , VAL O:229 , ASP O:231 , ASP P:301
BINDING SITE FOR RESIDUE CA O 344
52
FC7
SOFTWARE
GLY O:206 , THR O:214 , PHE O:215 , GLU O:216 , ASP P:95
BINDING SITE FOR RESIDUE CA O 345
53
FC8
SOFTWARE
GLN P:177 , ASP P:179 , ASP P:228 , VAL P:229 , ASP P:231 , ASP Q:301
BINDING SITE FOR RESIDUE CA P 346
54
FC9
SOFTWARE
GLY P:206 , THR P:214 , PHE P:215 , GLU P:216 , ASP Q:95
BINDING SITE FOR RESIDUE CA P 347
[
close Site info
]
SAPs(SNPs)/Variants
(1, 780)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_VP7_ROTRH_002 (T171T, chain B/F/G/H/I/J/K/L/M/N/O/P/Q, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_VP7_ROTRH_002
*
A
171
T
VP7_ROTRH
---
---
B/F/G/H/I/J/K/L/M/N/O/P/Q
T
171
T
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain X
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
Asymmetric Unit 5
Asymmetric Unit 6
Asymmetric Unit 7
Asymmetric Unit 8
Asymmetric Unit 9
Asymmetric Unit 10
Asymmetric Unit 11
Asymmetric Unit 12
Asymmetric Unit 13
Asymmetric Unit 14
Asymmetric Unit 15
Asymmetric Unit 16
Asymmetric Unit 17
Asymmetric Unit 18
Asymmetric Unit 19
Asymmetric Unit 20
Asymmetric Unit 21
Asymmetric Unit 22
Asymmetric Unit 23
Asymmetric Unit 24
Asymmetric Unit 25
Asymmetric Unit 26
Asymmetric Unit 27
Asymmetric Unit 28
Asymmetric Unit 29
Asymmetric Unit 30
Asymmetric Unit 31
Asymmetric Unit 32
Asymmetric Unit 33
Asymmetric Unit 34
Asymmetric Unit 35
Asymmetric Unit 36
Asymmetric Unit 37
Asymmetric Unit 38
Asymmetric Unit 39
Asymmetric Unit 40
Asymmetric Unit 41
Asymmetric Unit 42
Asymmetric Unit 43
Asymmetric Unit 44
Asymmetric Unit 45
Asymmetric Unit 46
Asymmetric Unit 47
Asymmetric Unit 48
Asymmetric Unit 49
Asymmetric Unit 50
Asymmetric Unit 51
Asymmetric Unit 52
Asymmetric Unit 53
Asymmetric Unit 54
Asymmetric Unit 55
Asymmetric Unit 56
Asymmetric Unit 57
Asymmetric Unit 58
Asymmetric Unit 59
Asymmetric Unit 60
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Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (506 KB)
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