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3CSY
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (759 KB)
Biol.Unit 2 (755 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE TRIMERIC PREFUSION EBOLA VIRUS GLYCOPROTEIN IN COMPLEX WITH A NEUTRALIZING ANTIBODY FROM A HUMAN SURVIVOR
Authors
:
J. E. Lee, M. L. Fusco, A. J. Hessell, W. B. Oswald, D. R. Burton, E. O. Saph
Date
:
10 Apr 08 (Deposition) - 08 Jul 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,I,J,K,L,M,N (1x)
Biol. Unit 2: G,H,O,P (3x)
Keywords
:
Glycoprotein-Antibody Complex, Immune System-Viral Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. E. Lee, M. L. Fusco, A. J. Hessell, W. B. Oswald, D. R. Burton, E. O. Saphire
Structure Of The Ebola Virus Glycoprotein Bound To An Antibody From A Human Survivor.
Nature V. 454 177 2008
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Hetero Components
(4, 53)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
2g: ALPHA-D-MANNOSE (MANg)
2h: ALPHA-D-MANNOSE (MANh)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
4o: N-ACETYL-D-GLUCOSAMINE (NAGo)
4p: N-ACETYL-D-GLUCOSAMINE (NAGp)
4q: N-ACETYL-D-GLUCOSAMINE (NAGq)
4r: N-ACETYL-D-GLUCOSAMINE (NAGr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
7
Ligand/Ion
BETA-D-MANNOSE
2
MAN
8
Ligand/Ion
ALPHA-D-MANNOSE
3
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
4
NAG
18
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(15, 15)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC4 (SOFTWARE)
14: CC5 (SOFTWARE)
15: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU I:254 , ASN I:257 , TYR I:261
BINDING SITE FOR RESIDUE NAG I 351
02
AC3
SOFTWARE
LEU I:70 , GLU I:156 , ALA I:158 , GLN J:508 , ASN J:563
BINDING SITE FOR RESIDUE NAG J 701
03
AC6
SOFTWARE
PHE L:535
BINDING SITE FOR RESIDUE MAN J 704
04
AC8
SOFTWARE
ASN K:257
BINDING SITE FOR RESIDUE NAG K 351
05
AC9
SOFTWARE
LEU K:70 , GLU K:156 , ALA K:158 , GLN L:508 , ASN L:563 , THR L:566
BINDING SITE FOR RESIDUE NAG L 701
06
BC3
SOFTWARE
LEU N:529
BINDING SITE FOR RESIDUE MAN L 704
07
BC5
SOFTWARE
LEU M:254 , ASN M:257 , TYR M:261
BINDING SITE FOR RESIDUE NAG M 351
08
BC6
SOFTWARE
GLU H:17
BINDING SITE FOR RESIDUE NAG M 352
09
BC7
SOFTWARE
LEU M:70 , GLU M:156 , ALA M:158 , GLN N:508 , ASN N:563
BINDING SITE FOR RESIDUE NAG N 701
10
BC8
SOFTWARE
GLU M:156 , PRO N:509
BINDING SITE FOR RESIDUE NAG N 702
11
CC1
SOFTWARE
LEU J:529
BINDING SITE FOR RESIDUE MAN N 704
12
CC2
SOFTWARE
ASN O:257 , TYR O:261
BINDING SITE FOR RESIDUE NAG O 351
13
CC4
SOFTWARE
LEU O:70 , GLU O:156 , ALA O:158 , GLN P:508 , ASN P:563
BINDING SITE FOR RESIDUE NAG P 701
14
CC5
SOFTWARE
PRO P:509
BINDING SITE FOR RESIDUE NAG P 702
15
CC7
SOFTWARE
PHE P:535
BINDING SITE FOR RESIDUE MAN P 704
[
close Site info
]
SAPs(SNPs)/Variants
(5, 20)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_VGP_EBOZM_001 (S65P, chain I/K/M/O, )
2: VAR_066403 (W148R, chain B/D/F/H, )
3: VAR_003897 (V191L, chain B/D/F/H, )
4: VAR_VGP_EBOZM_002 (S246P, chain I/K/M/O, )
5: VAR_VGP_EBOZM_003 (T544T, chain J/L/N/P, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_VGP_EBOZM_001
*
S
65
P
VGP_EBOZM
---
---
I/K/M/O
S
65
P
2
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
B/D/F/H
W
148
R
3
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
B/D/F/H
V
191
L
4
UniProt
VAR_VGP_EBOZM_002
*
S
246
P
VGP_EBOZM
---
---
I/K/M/O
S
246
P
5
UniProt
VAR_VGP_EBOZM_003
*
I
544
T
VGP_EBOZM
---
---
J/L/N/P
T
544
T
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:192-198,D:192-198,F:192-198,H:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
4
B:192-198
D:192-198
F:192-198
H:192-198
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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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
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CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_3csyB02 (B:108-211)
1b: CATH_3csyA02 (A:114-228)
1c: CATH_3csyC02 (C:114-228)
1d: CATH_3csyE02 (E:114-228)
1e: CATH_3csyG02 (G:114-228)
1f: CATH_3csyB01 (B:1-107)
1g: CATH_3csyD01 (D:1-107)
1h: CATH_3csyF01 (F:1-107)
1i: CATH_3csyH01 (H:1-107)
1j: CATH_3csyA01 (A:1-113)
1k: CATH_3csyC01 (C:1-113)
1l: CATH_3csyE01 (E:1-113)
1m: CATH_3csyG01 (G:1-113)
1n: CATH_3csyD02 (D:108-211)
1o: CATH_3csyF02 (F:108-211)
1p: CATH_3csyH02 (H:108-211)
View:
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Classes
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)
(
)
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(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
3csyB02
B:108-211
1b
3csyA02
A:114-228
1c
3csyC02
C:114-228
1d
3csyE02
E:114-228
1e
3csyG02
G:114-228
1f
3csyB01
B:1-107
1g
3csyD01
D:1-107
1h
3csyF01
F:1-107
1i
3csyH01
H:1-107
1j
3csyA01
A:1-113
1k
3csyC01
C:1-113
1l
3csyE01
E:1-113
1m
3csyG01
G:1-113
1n
3csyD02
D:108-211
1o
3csyF02
F:108-211
1p
3csyH02
H:108-211
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Pfam Domains
(0, 0)
Info
all PFAM domains
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