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3HE7
Asym. Unit
Info
Asym.Unit (140 KB)
Biol.Unit 1 (135 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MOUSE CD1D-ALPHA-GALACTOSYLCERAMIDE WITH MOUSE VALPHA14-VBETA7 NKT TCR
Authors
:
O. Patel, J. Rossjohn
Date
:
08 May 09 (Deposition) - 28 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Mouse Cd1D, Mouse Nkt T-Cell Receptors, Cell Membrane, Disulfide Bond, Endosome, Glycoprotein, Immune Response, Immunoglobulin Domain, Innate Immunity, Lysosome, Membrane, Transmembrane, Mhc I, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. G. Pellicci, O. Patel, L. Kjer-Nielsen, S. S. Pang, L. C. Sullivan, K. Kyparissoudis, A. G. Brooks, H. H. Reid, S. Gras, I. S. Lucet, R. Koh, M. J. Smyth, T. Mallevaey, J. L. Matsuda, L. Gapin, J. Mccluskey, D. I. Godfrey, J. Rossjohn
Differential Recognition Of Cd1D-Alpha-Galactosyl Ceramide By The V Beta 8. 2 And V Beta 7 Semi-Invariant Nkt T Cell Receptors
Immunity V. 31 47 2009
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOP... (AGHa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AGH
1
Ligand/Ion
N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:20 , TRP A:23
BINDING SITE FOR RESIDUE NAG A 303
2
AC2
SOFTWARE
TRP A:23 , SER A:24 , ASN A:42
BINDING SITE FOR RESIDUE NAG A 304
3
AC3
SOFTWARE
GLY A:130 , THR A:131 , GLN A:161 , ASN A:165 , NAG A:306
BINDING SITE FOR RESIDUE NAG A 305
4
AC4
SOFTWARE
TRP A:129 , GLY A:130 , THR A:131 , NAG A:305
BINDING SITE FOR RESIDUE NAG A 306
5
AC5
SOFTWARE
SER A:28 , PHE A:70 , TYR A:73 , SER A:76 , ASP A:80 , VAL A:118 , PHE A:120 , LEU A:143 , ASP A:153 , GLY A:155 , THR A:156 , THR A:159 , VAL A:160 , PHE A:171 , HOH A:314 , PRO C:28 , ASN C:30 , ARG C:95 , GLY C:96
BINDING SITE FOR RESIDUE AGH A 307
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SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_B2MG_MOUSE_002 (H34Q, chain B, )
2: VAR_B2MG_MOUSE_003 (K44E, chain B, )
3: VAR_B2MG_MOUSE_004 (R81T, chain B, )
4: VAR_B2MG_MOUSE_005 (A85D, chain B, )
5: VAR_B2MG_MOUSE_006 (A85V, chain B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_B2MG_MOUSE_002
*
H
54
Q
B2MG_MOUSE
---
---
B
H
34
Q
2
UniProt
VAR_B2MG_MOUSE_003
*
K
64
E
B2MG_MOUSE
---
---
B
K
44
E
3
UniProt
VAR_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B
R
81
T
4
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B
A
85
D
5
UniProt
VAR_B2MG_MOUSE_006
*
A
105
V
B2MG_MOUSE
---
---
B
A
85
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84)
;
View:
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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.
B2MG_MOUSE
98-104
1
B:78-84
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(4, 7)
Info
All SCOP Domains
1a: SCOP_d3he7a2 (A:186-299)
1b: SCOP_d3he7c1 (C:1-117)
1c: SCOP_d3he7d1 (D:2-118)
1d: SCOP_d3he7d2 (D:119-247)
2a: SCOP_d3he7c2 (C:118-207)
3a: SCOP_d3he7b_ (B:)
4a: SCOP_d3he7a1 (A:8-185)
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(
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d3he7a2
A:186-299
1b
d3he7c1
C:1-117
1c
d3he7d1
D:2-118
1d
d3he7d2
D:119-247
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d3he7c2
C:118-207
Protein domain
:
beta2-microglobulin
(530)
Mouse (Mus musculus) [TaxId: 10090]
(166)
3a
d3he7b_
B:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
automated matches
(52)
Protein domain
:
automated matches
(52)
Mouse (Mus musculus) [TaxId: 10090]
(29)
4a
d3he7a1
A:8-185
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3he7A01 (A:8-184)
2a: CATH_3he7B00 (B:2-99)
2b: CATH_3he7C01 (C:1-116)
2c: CATH_3he7A02 (A:185-280)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
Mouse (Mus musculus)
(40)
1a
3he7A01
A:8-184
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Mouse (Mus musculus)
(152)
2a
3he7B00
B:2-99
2b
3he7C01
C:1-116
2c
3he7A02
A:185-280
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain D
Asymmetric Unit 1
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