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1RER
Biol. Unit 2
Info
Asym.Unit (200 KB)
Biol.Unit 1 (193 KB)
Biol.Unit 2 (382 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE HOMOTRIMER OF FUSION GLYCOPROTEIN E1 FROM SEMLIKI FOREST VIRUS.
Authors
:
D. L. Gibbons, M. C. Vaney, A. Roussel, A. Vigouroux, B. Reilly, M. Kieli F. A. Rey
Date
:
07 Nov 03 (Deposition) - 27 Jan 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: A,B,C (2x)
Keywords
:
Envelope Glycoprotein, Membrane Fusion, Virus. , Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. L. Gibbons, M. C. Vaney, A. Roussel, A. Vigouroux, B. Reilly, J. Lepault, M. Kielian, F. A. Rey
Conformational Change And Protein-Protein Interactions Of The Fusion Protein Of Semliki Forest Virus.
Nature V. 427 320 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(7, 32)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: BROMIDE ION (BRa)
2b: BROMIDE ION (BRb)
2c: BROMIDE ION (BRc)
3a: ALPHA-L-FUCOSE (FUCa)
4a: BETA-L-FUCOSE (FULa)
5a: HOLMIUM ATOM (HOa)
5b: HOLMIUM ATOM (HOb)
5c: HOLMIUM ATOM (HOc)
5d: HOLMIUM ATOM (HOd)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
8a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
9a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
6
Ligand/Ion
BETA-D-MANNOSE
2
BR
-1
Ligand/Ion
BROMIDE ION
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
FUL
2
Ligand/Ion
BETA-L-FUCOSE
5
HO
-1
Ligand/Ion
HOLMIUM ATOM
6
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
9
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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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
MET A:136 , ASN A:141 , FUL A:402 , NAG A:403 , ARG B:134 , ASN B:141 , THR B:143 , NDG B:401 , FUC B:402
BINDING SITE FOR RESIDUE NAG A 401
02
AC2
SOFTWARE
GLN A:32 , MET A:136 , NAG A:401 , NAG B:403 , BMA B:404
BINDING SITE FOR RESIDUE FUL A 402
03
AC3
SOFTWARE
NAG A:401 , BMA A:404 , NAG A:409 , FUC B:402
BINDING SITE FOR RESIDUE NAG A 403
04
AC4
SOFTWARE
NAG A:403 , BMA A:408 , NAG A:409
BINDING SITE FOR RESIDUE BMA A 404
05
AC5
SOFTWARE
BMA A:404 , NAG A:409 , BMA B:404
BINDING SITE FOR RESIDUE BMA A 408
06
AC6
SOFTWARE
NAG A:403 , BMA A:404 , BMA A:408
BINDING SITE FOR RESIDUE NAG A 409
07
AC7
SOFTWARE
ARG A:134 , THR A:143 , NAG A:401 , ARG B:134 , MET B:136 , ASN B:141 , FUC B:402 , NAG B:403
BINDING SITE FOR RESIDUE NDG B 401
08
AC8
SOFTWARE
ARG A:134 , NAG A:401 , NAG A:403 , ARG B:134 , NDG B:401 , NAG B:403 , HOH B:440
BINDING SITE FOR RESIDUE FUC B 402
09
AC9
SOFTWARE
ARG A:134 , FUL A:402 , NDG B:401 , FUC B:402 , BMA B:404
BINDING SITE FOR RESIDUE NAG B 403
10
BC1
SOFTWARE
FUL A:402 , BMA A:408 , NAG B:403 , MAN B:405 , MAN B:408
BINDING SITE FOR RESIDUE BMA B 404
11
BC2
SOFTWARE
BMA B:404
BINDING SITE FOR RESIDUE MAN B 405
12
BC3
SOFTWARE
BMA B:404 , NAG B:409
BINDING SITE FOR RESIDUE MAN B 408
13
BC4
SOFTWARE
LYS A:345 , MAN B:408
BINDING SITE FOR RESIDUE NAG B 409
14
BC5
SOFTWARE
MET C:136 , ASN C:141 , NAG C:403
BINDING SITE FOR RESIDUE NAG C 401
15
BC6
SOFTWARE
NAG C:401
BINDING SITE FOR RESIDUE NAG C 403
16
BC7
SOFTWARE
SER A:168 , SER B:168 , ALA B:169 , SER C:168 , ALA C:169
BINDING SITE FOR RESIDUE PO4 B 415
17
BC8
SOFTWARE
PRO A:191
BINDING SITE FOR RESIDUE BR A 417
18
BC9
SOFTWARE
ASP A:188 , ASP B:188 , ASP C:188 , HOH C:455
BINDING SITE FOR RESIDUE HO A 411
19
CC1
SOFTWARE
TYR A:390 , ALA A:391 , GLU C:72
BINDING SITE FOR RESIDUE HO A 412
20
CC2
SOFTWARE
GLU A:72 , TYR B:390 , ALA B:391
BINDING SITE FOR RESIDUE HO B 413
21
CC3
SOFTWARE
GLU B:72 , TYR C:390 , ALA C:391
BINDING SITE FOR RESIDUE HO C 414
[
close Site info
]
SAPs(SNPs)/Variants
(8, 48)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_POLS_SFV_014 (A65S, chain A/B/C, )
2: VAR_POLS_SFV_015 (R115K, chain A/B/C, )
3: VAR_POLS_SFV_016 (M228T, chain A/B/C, )
4: VAR_POLS_SFV_017 (I297T, chain A/B/C, )
5: VAR_POLS_SFV_018 (T319K, chain A/B/C, )
6: VAR_POLS_SFV_019 (N323D, chain A/B/C, )
7: VAR_POLS_SFV_020 (G350R, chain A/B/C, )
8: VAR_POLS_SFV_021 (R373K, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_POLS_SFV_014
*
A
880
S
POLS_SFV
---
---
A/B/C
A
65
S
2
UniProt
VAR_POLS_SFV_015
*
R
930
K
POLS_SFV
---
---
A/B/C
R
115
K
3
UniProt
VAR_POLS_SFV_016
*
M
1043
T
POLS_SFV
---
---
A/B/C
M
228
T
4
UniProt
VAR_POLS_SFV_017
*
I
1112
T
POLS_SFV
---
---
A/B/C
I
297
T
5
UniProt
VAR_POLS_SFV_018
*
T
1134
K
POLS_SFV
---
---
A/B/C
T
319
K
6
UniProt
VAR_POLS_SFV_019
*
N
1138
D
POLS_SFV
---
---
A/B/C
N
323
D
7
UniProt
VAR_POLS_SFV_020
*
G
1165
R
POLS_SFV
---
---
A/B/C
G
350
R
8
UniProt
VAR_POLS_SFV_021
*
R
1188
K
POLS_SFV
---
---
A/B/C
R
373
K
* 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:
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Label:
End label:
Sorry, no Info available
[
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1rera1 (A:293-391)
1b: SCOP_d1rerb1 (B:293-391)
1c: SCOP_d1rerc1 (C:293-391)
2a: SCOP_d1rera2 (A:1-292)
2b: SCOP_d1rerb2 (B:1-292)
2c: SCOP_d1rerc2 (C:1-292)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
Class II viral fusion proteins C-terminal domain
(27)
Protein domain
:
Fusion glycoprotein E1
(3)
Semliki forest virus [TaxId: 11033]
(3)
1a
d1rera1
A:293-391
1b
d1rerb1
B:293-391
1c
d1rerc1
C:293-391
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Viral glycoprotein, central and dimerisation domains
(24)
Superfamily
:
Viral glycoprotein, central and dimerisation domains
(24)
Family
:
Viral glycoprotein, central and dimerisation domains
(17)
Protein domain
:
Fusion glycoprotein E1
(2)
Semliki forest virus [TaxId: 11033]
(2)
2a
d1rera2
A:1-292
2b
d1rerb2
B:1-292
2c
d1rerc2
C:1-292
[
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]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1rerA01 (A:1-42,A:124-173,A:257-290)
1b: CATH_1rerB01 (B:1-42,B:124-173,B:257-290)
1c: CATH_1rerC01 (C:1-42,C:124-173,C:257-290)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Tick-borne Encephalitis virus Glycoprotein; domain 1
(14)
Homologous Superfamily
:
Tick-borne Encephalitis virus Glycoprotein, domain 1
(14)
Semliki forest virus. Organism_taxid: 11033
(2)
1a
1rerA01
A:1-42,A:124-173,A:257-290
1b
1rerB01
B:1-42,B:124-173,B:257-290
1c
1rerC01
C:1-42,C:124-173,C:257-290
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Alpha_E1_glycop_1rerC01 (C:1-391)
1b: PFAM_Alpha_E1_glycop_1rerC02 (C:1-391)
1c: PFAM_Alpha_E1_glycop_1rerC03 (C:1-391)
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Clans
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)
(
)
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(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Alpha_E1_glycop]
(11)
Family
:
Alpha_E1_glycop
(11)
Semliki forest virus (SFV)
(1)
1a
Alpha_E1_glycop-1rerC01
C:1-391
1b
Alpha_E1_glycop-1rerC02
C:1-391
1c
Alpha_E1_glycop-1rerC03
C:1-391
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