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2J8U
Asym. Unit
Info
Asym.Unit (268 KB)
Biol.Unit 1 (130 KB)
Biol.Unit 2 (130 KB)
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(1)
Title
:
LARGE CDR3A LOOP ALTERATION AS A FUNCTION OF MHC MUTATION.
Authors
:
P. J. Miller, Y. P. Benhar, W. Biddison, E. J. Collins
Date
:
27 Oct 06 (Deposition) - 16 Oct 07 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.88
Chains
:
Asym. Unit : A,B,C,E,F,H,I,J,L,M
Biol. Unit 1: A,B,C,E,F (1x)
Biol. Unit 2: H,I,J,L,M (1x)
Keywords
:
Glycoprotein, Immune System, Transmembrane, Mhc I, Membrane, Secreted, Glycation, Immunoglobulin Domain, Host-Virus Interaction, Pyrrolidone Carboxylic Acid, Immune Response, Disease Mutation, Imunoregulatory Complex, Class I Mhc-Tcr Co-Crystal
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. J. Miller, Y. Pazy, B. Conti, D. Riddle, E. Appella, E. J. Collins
Single Mhc Mutation Eliminates Enthalpy Associated With T Cell Receptor Binding.
J. Mol. Biol. V. 373 315 2007
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Hetero Components
(0, 0)
Info
All Hetero Components
View:
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
View:
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Label:
Sorry, no Info available
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]
SAPs(SNPs)/Variants
(24, 48)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004334 (F9Y, chain A/H, )
02: VAR_004335 (D30N, chain A/H, )
03: VAR_016726 (A41G, chain A/H, )
04: VAR_004336 (Q43R, chain A/H, )
05: VAR_004337 (A66N, chain A/H, )
06: VAR_016727 (H70Q, chain A/H, )
07: VAR_004338 (T73I, chain A/H, )
08: VAR_016728 (H74D, chain A/H, )
09: VAR_004339 (V95L, chain A/H, )
10: VAR_004340 (R97M, chain A/H, )
11: VAR_004341 (Y99C, chain A/H, )
12: VAR_004342 (Y99F, chain A/H, )
13: VAR_004343 (W107G, chain A/H, )
14: VAR_TCA_MOUSE_001 (N117D, chain E/L, )
15: VAR_TCA_MOUSE_002 (N117N, chain E/L, )
16: VAR_004344 (M138K, chain A/H, )
17: VAR_004345 (A149T, chain A/H, )
18: VAR_004346 (V152E, chain A/H, )
19: VAR_004348 (L156Q, chain A/H, )
20: VAR_004347 (L156W, chain A/H, )
21: VAR_004349 (T163E, chain A/H, )
22: VAR_016729 (E166D, chain A/H, )
23: VAR_016730 (W167G, chain A/H, )
24: VAR_004350 (A236E, chain A/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004334
F
33
Y
1A02_HUMAN
Polymorphism
---
A/H
F
9
Y
02
UniProt
VAR_004335
D
54
N
1A02_HUMAN
Polymorphism
---
A/H
D
30
N
03
UniProt
VAR_016726
A
65
G
1A02_HUMAN
Polymorphism
---
A/H
A
41
G
04
UniProt
VAR_004336
Q
67
R
1A02_HUMAN
Polymorphism
---
A/H
Q
43
R
05
UniProt
VAR_004337
K
90
N
1A02_HUMAN
Polymorphism
---
A/H
A
66
N
06
UniProt
VAR_016727
H
94
Q
1A02_HUMAN
Polymorphism
---
A/H
H
70
Q
07
UniProt
VAR_004338
T
97
I
1A02_HUMAN
Polymorphism
---
A/H
T
73
I
08
UniProt
VAR_016728
H
98
D
1A02_HUMAN
Polymorphism
---
A/H
H
74
D
09
UniProt
VAR_004339
V
119
L
1A02_HUMAN
Polymorphism
---
A/H
V
95
L
10
UniProt
VAR_004340
R
121
M
1A02_HUMAN
Polymorphism
---
A/H
R
97
M
11
UniProt
VAR_004341
Y
123
C
1A02_HUMAN
Polymorphism
---
A/H
Y
99
C
12
UniProt
VAR_004342
Y
123
F
1A02_HUMAN
Polymorphism
---
A/H
Y
99
F
13
UniProt
VAR_004343
W
131
G
1A02_HUMAN
Polymorphism
---
A/H
W
107
G
14
UniProt
VAR_TCA_MOUSE_001
*
Y
2
D
TCA_MOUSE
---
---
E/L
N
117
D
15
UniProt
VAR_TCA_MOUSE_002
*
Y
2
N
TCA_MOUSE
---
---
E/L
N
117
N
16
UniProt
VAR_004344
M
162
K
1A02_HUMAN
Polymorphism
---
A/H
M
138
K
17
UniProt
VAR_004345
A
173
T
1A02_HUMAN
Polymorphism
---
A/H
A
149
T
18
UniProt
VAR_004346
V
176
E
1A02_HUMAN
Polymorphism
---
A/H
V
152
E
19
UniProt
VAR_004348
L
180
Q
1A02_HUMAN
Polymorphism
---
A/H
L
156
Q
20
UniProt
VAR_004347
L
180
W
1A02_HUMAN
Polymorphism
---
A/H
L
156
W
21
UniProt
VAR_004349
T
187
E
1A02_HUMAN
Polymorphism
---
A/H
T
163
E
22
UniProt
VAR_016729
E
190
D
1A02_HUMAN
Polymorphism
---
A/H
E
166
D
23
UniProt
VAR_016730
W
191
G
1A02_HUMAN
Polymorphism
---
A/H
W
167
G
24
UniProt
VAR_004350
A
260
E
1A02_HUMAN
Polymorphism
---
A/H
A
236
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,I:78-84,A:257-263,H:257-26...)
;
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.
B2MG_HUMAN
98-104
2
B:78-84
I:78-84
1A02_HUMAN
281-287
2
A:257-263
H:257-263
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Exons
(1, 2)
Info
All Exons
Exon 1.1a (C:1-9 | J:1-9)
View:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.3
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000256545
1a
ENSE00001232339
chr15:
34394149-34393805
345
EMC7_HUMAN
1-79
79
2
C:1-9
J:1-9
9
9
1.3
ENST00000256545
3
ENSE00000912984
chr15:
34388215-34388096
120
EMC7_HUMAN
79-119
41
0
-
-
1.4
ENST00000256545
4
ENSE00001043239
chr15:
34382656-34382518
139
EMC7_HUMAN
119-165
47
0
-
-
1.5
ENST00000256545
5
ENSE00001043245
chr15:
34380334-34380254
81
EMC7_HUMAN
166-192
27
0
-
-
1.6c
ENST00000256545
6c
ENSE00001232334
chr15:
34376687-34376218
470
EMC7_HUMAN
193-242
50
0
-
-
[
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]
SCOP Domains
(7, 14)
Info
All SCOP Domains
1a: SCOP_d2j8ub_ (B:)
1b: SCOP_d2j8ui_ (I:)
2a: SCOP_d2j8ua1 (A:182-275)
2b: SCOP_d2j8uh1 (H:182-275)
3a: SCOP_d2j8ue2 (E:118-198)
3b: SCOP_d2j8ul2 (L:118-198)
4a: SCOP_d2j8uf2 (F:118-245)
4b: SCOP_d2j8um2 (M:118-245)
5a: SCOP_d2j8ue1 (E:0-117)
5b: SCOP_d2j8ul1 (L:0-117)
6a: SCOP_d2j8uf1 (F:1-117)
6b: SCOP_d2j8um1 (M:1-117)
7a: SCOP_d2j8ua2 (A:1-181)
7b: SCOP_d2j8uh2 (H:1-181)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d2j8ub_
B:
1b
d2j8ui_
I:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d2j8ua1
A:182-275
2b
d2j8uh1
H:182-275
Protein domain
:
T-cell antigen receptor
(81)
Mouse (Mus musculus), alpha-chain [TaxId: 10090]
(11)
3a
d2j8ue2
E:118-198
3b
d2j8ul2
L:118-198
Mouse (Mus musculus), beta-chain [TaxId: 10090]
(15)
4a
d2j8uf2
F:118-245
4b
d2j8um2
M:118-245
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
T-cell antigen receptor
(105)
Mouse (Mus musculus), alpha-chain [TaxId: 10090]
(21)
5a
d2j8ue1
E:0-117
5b
d2j8ul1
L:0-117
Mouse (Mus musculus), beta-chain [TaxId: 10090]
(28)
6a
d2j8uf1
F:1-117
6b
d2j8um1
M:1-117
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class I MHC, alpha-1 and alpha-2 domains
(294)
Human (Homo sapiens), HLA-A2.1 [TaxId: 9606]
(92)
7a
d2j8ua2
A:1-181
7b
d2j8uh2
H:1-181
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2j8uA01 (A:1-181)
1b: CATH_2j8uH01 (H:1-181)
2a: CATH_2j8uB00 (B:0-99)
2b: CATH_2j8uI00 (I:0-99)
2c: CATH_2j8uF01 (F:3-117)
2d: CATH_2j8uM01 (M:3-117)
2e: CATH_2j8uF02 (F:118-245)
2f: CATH_2j8uM02 (M:118-245)
2g: CATH_2j8uE01 (E:1-116)
2h: CATH_2j8uL01 (L:1-116)
2i: CATH_2j8uA02 (A:182-270)
2j: CATH_2j8uH02 (H:182-270)
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Classes
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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)
[unclassified]
(2)
1a
2j8uA01
A:1-181
1b
2j8uH01
H:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
[unclassified]
(54)
2a
2j8uB00
B:0-99
2b
2j8uI00
I:0-99
2c
2j8uF01
F:3-117
2d
2j8uM01
M:3-117
2e
2j8uF02
F:118-245
2f
2j8uM02
M:118-245
2g
2j8uE01
E:1-116
2h
2j8uL01
L:1-116
2i
2j8uA02
A:182-270
2j
2j8uH02
H:182-270
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (268 KB)
Header - Asym.Unit
Biol.Unit 1 (130 KB)
Header - Biol.Unit 1
Biol.Unit 2 (130 KB)
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