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1UF2
Asym. Unit
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Asym.Unit (1.2 MB)
Biol.Unit 1, α-C (67.4 MB)
Biol.Unit 1 (67.4 MB)
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(1)
Title
:
THE ATOMIC STRUCTURE OF RICE DWARF VIRUS (RDV)
Authors
:
A. Nakagawa, N. Miyazaki, J. Taka, H. Naitow, A. Ogawa, Z. Fujimoto, H. Mizuno, T. Higashi, Y. Watanabe, T. Omura, R. H. Cheng, T. Tsukihara
Date
:
23 May 03 (Deposition) - 14 Oct 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,P,Q,R,S,T
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,P,Q,R,S,T (60x)
Keywords
:
Virus Components, Icosahedral Virus
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Nakagawa, N. Miyazaki, J. Taka, H. Naitow, A. Ogawa, Z. Fujimoto, H. Mizuno, T. Higashi, Y. Watanabe, T. Omura, R. H. Cheng, T. Tsukihara
The Atomic Structure Of Rice Dwarf Virus Reveals The Self-Assembly Mechanism Of Component Proteins.
Structure V. 11 1227 2003
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
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Sites
(0, 0)
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SAPs(SNPs)/Variants
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PROSITE Patterns/Profiles
(0, 0)
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Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 28)
Info
All SCOP Domains
1a: SCOP_d1uf2c1 (C:1-147,C:301-421)
1b: SCOP_d1uf2d1 (D:1-147,D:301-421)
1c: SCOP_d1uf2r1 (R:1-147,R:301-421)
1d: SCOP_d1uf2s1 (S:1-147,S:301-421)
1e: SCOP_d1uf2t1 (T:1-147,T:301-421)
1f: SCOP_d1uf2e1 (E:1-147,E:301-421)
1g: SCOP_d1uf2f1 (F:1-147,F:301-421)
1h: SCOP_d1uf2g1 (G:1-147,G:301-421)
1i: SCOP_d1uf2h1 (H:1-147,H:301-421)
1j: SCOP_d1uf2i1 (I:1-147,I:301-421)
1k: SCOP_d1uf2j1 (J:1-147,J:301-421)
1l: SCOP_d1uf2p1 (P:1-147,P:301-421)
1m: SCOP_d1uf2q1 (Q:1-147,Q:301-421)
2a: SCOP_d1uf2c2 (C:148-300)
2b: SCOP_d1uf2d2 (D:148-300)
2c: SCOP_d1uf2r2 (R:148-300)
2d: SCOP_d1uf2s2 (S:148-300)
2e: SCOP_d1uf2t2 (T:148-300)
2f: SCOP_d1uf2e2 (E:148-300)
2g: SCOP_d1uf2f2 (F:148-300)
2h: SCOP_d1uf2g2 (G:148-300)
2i: SCOP_d1uf2h2 (H:148-300)
2j: SCOP_d1uf2i2 (I:148-300)
2k: SCOP_d1uf2j2 (J:148-300)
2l: SCOP_d1uf2p2 (P:148-300)
2m: SCOP_d1uf2q2 (Q:148-300)
3a: SCOP_d1uf2a_ (A:)
3b: SCOP_d1uf2b_ (B:)
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)
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)
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)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
A virus capsid protein alpha-helical domain
(4)
Superfamily
:
A virus capsid protein alpha-helical domain
(4)
Family
:
Phytoreovirus capsid
(1)
Protein domain
:
RDV p8
(1)
Rice dwarf virus [TaxId: 10991]
(1)
1a
d1uf2c1
C:1-147,C:301-421
1b
d1uf2d1
D:1-147,D:301-421
1c
d1uf2r1
R:1-147,R:301-421
1d
d1uf2s1
S:1-147,S:301-421
1e
d1uf2t1
T:1-147,T:301-421
1f
d1uf2e1
E:1-147,E:301-421
1g
d1uf2f1
F:1-147,F:301-421
1h
d1uf2g1
G:1-147,G:301-421
1i
d1uf2h1
H:1-147,H:301-421
1j
d1uf2i1
I:1-147,I:301-421
1k
d1uf2j1
J:1-147,J:301-421
1l
d1uf2p1
P:1-147,P:301-421
1m
d1uf2q1
Q:1-147,Q:301-421
Class
:
All beta proteins
(24004)
Fold
:
Viral protein domain
(195)
Superfamily
:
Viral protein domain
(195)
Family
:
Top domain of virus capsid protein
(5)
Protein domain
:
RDV p8, central (top) domain
(2)
Rice dwarf virus [TaxId: 10991]
(1)
2a
d1uf2c2
C:148-300
2b
d1uf2d2
D:148-300
2c
d1uf2r2
R:148-300
2d
d1uf2s2
S:148-300
2e
d1uf2t2
T:148-300
2f
d1uf2e2
E:148-300
2g
d1uf2f2
F:148-300
2h
d1uf2g2
G:148-300
2i
d1uf2h2
H:148-300
2j
d1uf2i2
I:148-300
2k
d1uf2j2
J:148-300
2l
d1uf2p2
P:148-300
2m
d1uf2q2
Q:148-300
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Reovirus inner layer core protein p3
(2)
Superfamily
:
Reovirus inner layer core protein p3
(2)
Family
:
Phytoreovirus core
(1)
Protein domain
:
RDV p3
(1)
Rice dwarf virus [TaxId: 10991]
(1)
3a
d1uf2a_
A:
3b
d1uf2b_
B:
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CATH Domains
(1, 13)
Info
all CATH domains
1a: CATH_1uf2C02 (C:146-302)
1b: CATH_1uf2D02 (D:146-302)
1c: CATH_1uf2R02 (R:146-302)
1d: CATH_1uf2S02 (S:146-302)
1e: CATH_1uf2T02 (T:146-302)
1f: CATH_1uf2E02 (E:146-302)
1g: CATH_1uf2F02 (F:146-302)
1h: CATH_1uf2G02 (G:146-302)
1i: CATH_1uf2H02 (H:146-302)
1j: CATH_1uf2I02 (I:146-302)
1k: CATH_1uf2J02 (J:146-302)
1l: CATH_1uf2P02 (P:146-302)
1m: CATH_1uf2Q02 (Q:146-302)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.170, no name defined]
(7)
Rice dwarf virus. Organism_taxid: 10991. Strain: o strain.
(1)
1a
1uf2C02
C:146-302
1b
1uf2D02
D:146-302
1c
1uf2R02
R:146-302
1d
1uf2S02
S:146-302
1e
1uf2T02
T:146-302
1f
1uf2E02
E:146-302
1g
1uf2F02
F:146-302
1h
1uf2G02
G:146-302
1i
1uf2H02
H:146-302
1j
1uf2I02
I:146-302
1k
1uf2J02
J:146-302
1l
1uf2P02
P:146-302
1m
1uf2Q02
Q:146-302
[
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Pfam Domains
(3, 16)
Info
all PFAM domains
1a: PFAM_Phytoreo_P8_1uf2T01 (T:1-421)
1b: PFAM_Phytoreo_P8_1uf2T02 (T:1-421)
1c: PFAM_Phytoreo_P8_1uf2T03 (T:1-421)
1d: PFAM_Phytoreo_P8_1uf2T04 (T:1-421)
1e: PFAM_Phytoreo_P8_1uf2T05 (T:1-421)
1f: PFAM_Phytoreo_P8_1uf2T06 (T:1-421)
1g: PFAM_Phytoreo_P8_1uf2T07 (T:1-421)
1h: PFAM_Phytoreo_P8_1uf2T08 (T:1-421)
1i: PFAM_Phytoreo_P8_1uf2T09 (T:1-421)
1j: PFAM_Phytoreo_P8_1uf2T10 (T:1-421)
1k: PFAM_Phytoreo_P8_1uf2T11 (T:1-421)
1l: PFAM_Phytoreo_P8_1uf2T12 (T:1-421)
1m: PFAM_Phytoreo_P8_1uf2T13 (T:1-421)
2a: PFAM_Phytoreo_S7_1uf2K01 (K:289-300)
3a: PFAM_RDV_p3_1uf2B01 (B:50-1012)
3b: PFAM_RDV_p3_1uf2B02 (B:50-1012)
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Clans
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)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Phytoreo_P8]
(1)
Family
:
Phytoreo_P8
(1)
Rice dwarf virus (isolate O) (RDV)
(1)
1a
Phytoreo_P8-1uf2T01
T:1-421
1b
Phytoreo_P8-1uf2T02
T:1-421
1c
Phytoreo_P8-1uf2T03
T:1-421
1d
Phytoreo_P8-1uf2T04
T:1-421
1e
Phytoreo_P8-1uf2T05
T:1-421
1f
Phytoreo_P8-1uf2T06
T:1-421
1g
Phytoreo_P8-1uf2T07
T:1-421
1h
Phytoreo_P8-1uf2T08
T:1-421
1i
Phytoreo_P8-1uf2T09
T:1-421
1j
Phytoreo_P8-1uf2T10
T:1-421
1k
Phytoreo_P8-1uf2T11
T:1-421
1l
Phytoreo_P8-1uf2T12
T:1-421
1m
Phytoreo_P8-1uf2T13
T:1-421
Clan
:
no clan defined [family: Phytoreo_S7]
(1)
Family
:
Phytoreo_S7
(1)
Rice dwarf virus (isolate O) (RDV)
(1)
2a
Phytoreo_S7-1uf2K01
K:289-300
Clan
:
no clan defined [family: RDV-p3]
(1)
Family
:
RDV-p3
(1)
Rice dwarf virus (isolate Akita) (RDV)
(1)
3a
RDV-p3-1uf2B01
B:50-1012
3b
RDV-p3-1uf2B02
B:50-1012
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Asym.Unit (1.2 MB)
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