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3PGC
Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (65 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HLA-DR1 WITH CLIP106-120, FLIPPED PEPTIDE ORIENTATION
Authors
:
S. Gunther, A. Schlundt, J. Sticht, Y. Roske, U. Heinemann, K. -H. Wiesm G. Jung, K. Falk, O. Rotzschke, C. Freund
Date
:
01 Nov 10 (Deposition) - 08 Dec 10 (Release) - 05 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.66
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Mhc Class Ii, Mhc Ii, Immune System, Self Antigen, Invariant Chain, Clip
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Gunther, A. Schlundt, J. Sticht, Y. Roske, U. Heinemann, K. H. Wiesmuller, G. Jung, K. Falk, O. Rotzschke, C. Freund
Bidirectional Binding Of Invariant Chain Peptides To An Mhc Class Ii Molecule.
Proc. Natl. Acad. Sci. Usa V. 107 22219 2010
[
close entry info
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU D:4
BINDING SITE FOR RESIDUE PEG D 193
2
AC2
SOFTWARE
LEU D:45 , GLU D:46 , GLU D:47 , ARG E:93
BINDING SITE FOR RESIDUE GOL D 194
[
close Site info
]
SAPs(SNPs)/Variants
(25, 50)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_033379 (R4K, chain B/E, )
02: VAR_033380 (R4Q, chain B/E, )
03: VAR_016740 (Q10E, chain B/E, )
04: VAR_033381 (S37Y, chain B/E, )
05: VAR_016741 (G45R, chain B/E, )
06: VAR_033382 (Y47F, chain B/E, )
07: VAR_033383 (Y60S, chain B/E, )
08: VAR_016710 (L67I, chain B/E, )
09: VAR_016711 (Q70D, chain B/E, )
10: VAR_033384 (Q70E, chain B/E, )
11: VAR_033385 (Q70H, chain B/E, )
12: VAR_016742 (R71A, chain B/E, )
13: VAR_016712 (R71E, chain B/E, )
14: VAR_033386 (A73G, chain B/E, )
15: VAR_033387 (A74E, chain B/E, )
16: VAR_016713 (T77N, chain B/E, )
17: VAR_033388 (Y78H, chain B/E, )
18: VAR_016714 (V85A, chain B/E, )
19: VAR_016715 (G86V, chain B/E, )
20: VAR_033389 (G135D, chain B/E, )
21: VAR_033390 (A140T, chain B/E, )
22: VAR_033391 (V142M, chain B/E, )
23: VAR_033392 (Q149H, chain B/E, )
24: VAR_033393 (R166Q, chain B/E, )
25: VAR_033394 (T181I, chain B/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_033379
R
33
K
2B11_HUMAN
Polymorphism
34716432
B/E
R
4
K
02
UniProt
VAR_033380
R
33
Q
2B11_HUMAN
Polymorphism
34716432
B/E
R
4
Q
03
UniProt
VAR_016740
Q
39
E
2B11_HUMAN
Polymorphism
---
B/E
Q
10
E
04
UniProt
VAR_033381
S
66
Y
2B11_HUMAN
Polymorphism
16822820
B/E
S
37
Y
05
UniProt
VAR_016741
G
74
R
2B11_HUMAN
Polymorphism
---
B/E
G
45
R
06
UniProt
VAR_033382
Y
76
F
2B11_HUMAN
Polymorphism
1060346
B/E
Y
47
F
07
UniProt
VAR_033383
Y
89
S
2B11_HUMAN
Polymorphism
36074728
B/E
Y
60
S
08
UniProt
VAR_016710
L
96
I
2B11_HUMAN
Polymorphism
---
B/E
L
67
I
09
UniProt
VAR_016711
Q
99
D
2B11_HUMAN
Polymorphism
---
B/E
Q
70
D
10
UniProt
VAR_033384
Q
99
E
2B11_HUMAN
Polymorphism
17881965
B/E
Q
70
E
11
UniProt
VAR_033385
Q
99
H
2B11_HUMAN
Polymorphism
17879599
B/E
Q
70
H
12
UniProt
VAR_016742
R
100
A
2B11_HUMAN
Polymorphism
---
B/E
R
71
A
13
UniProt
VAR_016712
R
100
E
2B11_HUMAN
Polymorphism
---
B/E
R
71
E
14
UniProt
VAR_033386
A
102
G
2B11_HUMAN
Polymorphism
17878857
B/E
A
73
G
15
UniProt
VAR_033387
A
103
E
2B11_HUMAN
Polymorphism
16822805
B/E
A
74
E
16
UniProt
VAR_016713
T
106
N
2B11_HUMAN
Polymorphism
16822752
B/E
T
77
N
17
UniProt
VAR_033388
Y
107
H
2B11_HUMAN
Polymorphism
16822512
B/E
Y
78
H
18
UniProt
VAR_016714
V
114
A
2B11_HUMAN
Polymorphism
17424145
B/E
V
85
A
19
UniProt
VAR_016715
G
115
V
2B11_HUMAN
Polymorphism
2230810
B/E
G
86
V
20
UniProt
VAR_033389
G
164
D
2B11_HUMAN
Polymorphism
1059633
B/E
G
135
D
21
UniProt
VAR_033390
A
169
T
2B11_HUMAN
Polymorphism
2308768
B/E
A
140
T
22
UniProt
VAR_033391
V
171
M
2B11_HUMAN
Polymorphism
701829
B/E
V
142
M
23
UniProt
VAR_033392
Q
178
H
2B11_HUMAN
Polymorphism
701830
B/E
Q
149
H
24
UniProt
VAR_033393
R
195
Q
2B11_HUMAN
Polymorphism
3205588
B/E
R
166
Q
25
UniProt
VAR_033394
T
210
I
2B11_HUMAN
Polymorphism
17423930
B/E
T
181
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:161-167,D:161-167,B:171-177,E:17...)
;
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.
DRA_HUMAN
186-192
2
A:161-167
D:161-167
2B11_HUMAN
200-206
2
B:171-177
E:171-177
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.2c (C:106-120 | F:106-120)
Exon 2.3 (B:1-5 | E:2-5)
Exon 2.4 (B:5-95 | E:5-95)
Exon 2.5b (B:95-189 (gaps) | E:95-189 (gaps))
Exon 2.6 (B:189-192 | E:189-189)
Exon 3.7b (A:4-85 | D:4-85)
Exon 3.8c (A:85-179 | D:85-179)
Exon 3.9a (A:179-180 | D:179-181)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2a/1.2c
02: Boundary 1.2c/1.3a
03: Boundary -/2.3
04: Boundary 2.3/2.4
05: Boundary 2.4/2.5b
06: Boundary 2.5b/2.6
07: Boundary 2.6/2.7
08: Boundary 3.6a/3.7b
09: Boundary 3.7b/3.8c
10: Boundary 3.8c/3.9a
11: Boundary 3.9a/3.10b
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
1.1d
ENST00000009530
1d
ENSE00002143935
chr5:
149792314-149792188
127
HG2A_HUMAN
1-42
42
0
-
-
1.2a
ENST00000009530
2a
ENSE00000767447
chr5:
149786887-149786715
173
HG2A_HUMAN
42-100
59
0
-
-
1.2c
ENST00000009530
2c
ENSE00000439662
chr5:
149786523-149786444
80
HG2A_HUMAN
100-126
27
2
C:106-120
F:106-120
15
15
1.3a
ENST00000009530
3a
ENSE00000767449
chr5:
149785884-149785822
63
HG2A_HUMAN
127-147
21
0
-
-
1.5
ENST00000009530
5
ENSE00000767450
chr5:
149784743-149784648
96
HG2A_HUMAN
148-179
32
0
-
-
1.6a
ENST00000009530
6a
ENSE00000841201
chr5:
149784330-149784243
88
HG2A_HUMAN
180-209
30
0
-
-
1.7
ENST00000009530
7
ENSE00000767452
chr5:
149782875-149782684
192
HG2A_HUMAN
209-273
65
0
-
-
1.8a
ENST00000009530
8a
ENSE00001673543
chr5:
149782188-149782126
63
HG2A_HUMAN
273-294
22
0
-
-
1.8d
ENST00000009530
8d
ENSE00002129676
chr5:
149781813-149781715
99
HG2A_HUMAN
294-296
3
0
-
-
2.3
ENST00000360004
3
ENSE00001930619
chr6:
32557625-32557420
206
2B11_HUMAN
1-34
34
2
B:1-5
E:2-5
5
4
2.4
ENST00000360004
4
ENSE00001731226
chr6:
32552155-32551886
270
2B11_HUMAN
34-124
91
2
B:5-95
E:5-95
91
91
2.5b
ENST00000360004
5b
ENSE00001801024
chr6:
32549615-32549334
282
2B11_HUMAN
124-218
95
2
B:95-189 (gaps)
E:95-189 (gaps)
95
95
2.6
ENST00000360004
6
ENSE00001717727
chr6:
32548633-32548523
111
2B11_HUMAN
218-255
38
2
B:189-192
E:189-189
4
1
2.7
ENST00000360004
7
ENSE00001773376
chr6:
32548047-32548024
24
2B11_HUMAN
255-263
9
0
-
-
2.8
ENST00000360004
8
ENSE00001954617
chr6:
32546881-32546546
336
2B11_HUMAN
263-266
4
0
-
-
3.6a
ENST00000383259
6a
ENSE00001839042
HSCHR6_MHC_QBL:32365090-32365280
191
DRA_HUMAN
1-28
28
0
-
-
3.7b
ENST00000383259
7b
ENSE00001719010
HSCHR6_MHC_QBL:32367694-32367939
246
DRA_HUMAN
28-110
83
2
A:4-85
D:4-85
82
82
3.8c
ENST00000383259
8c
ENSE00001737588
HSCHR6_MHC_QBL:32368431-32368712
282
DRA_HUMAN
110-204
95
2
A:85-179
D:85-179
95
95
3.9a
ENST00000383259
9a
ENSE00001770912
HSCHR6_MHC_QBL:32369002-32369167
166
DRA_HUMAN
204-254
51
2
A:179-180
D:179-181
2
3
3.10b
ENST00000383259
10b
ENSE00001925700
HSCHR6_MHC_QBL:32369906-32370300
395
DRA_HUMAN
-
0
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
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Pfam Domains
(4, 10)
Info
all PFAM domains
1a: PFAM_C1_set_3pgcE01 (E:103-185)
1b: PFAM_C1_set_3pgcE02 (E:103-185)
1c: PFAM_C1_set_3pgcD01 (D:93-175)
1d: PFAM_C1_set_3pgcD02 (D:93-175)
2a: PFAM_MHC_II_alpha_3pgcD03 (D:4-84)
2b: PFAM_MHC_II_alpha_3pgcD04 (D:4-84)
3a: PFAM_MHC_II_beta_3pgcE03 (E:13-87)
3b: PFAM_MHC_II_beta_3pgcE04 (E:13-87)
4a: PFAM_MHC2_interact_3pgcF01 (F:106-120)
4b: PFAM_MHC2_interact_3pgcF02 (F:106-120)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-3pgcE01
E:103-185
1b
C1-set-3pgcE02
E:103-185
1c
C1-set-3pgcD01
D:93-175
1d
C1-set-3pgcD02
D:93-175
Clan
:
MHC
(252)
Family
:
MHC_II_alpha
(42)
Homo sapiens (Human)
(26)
2a
MHC_II_alpha-3pgcD03
D:4-84
2b
MHC_II_alpha-3pgcD04
D:4-84
Family
:
MHC_II_beta
(39)
Homo sapiens (Human)
(25)
3a
MHC_II_beta-3pgcE03
E:13-87
3b
MHC_II_beta-3pgcE04
E:13-87
Clan
:
no clan defined [family: MHC2-interact]
(4)
Family
:
MHC2-interact
(4)
Homo sapiens (Human)
(4)
4a
MHC2-interact-3pgcF01
F:106-120
4b
MHC2-interact-3pgcF02
F:106-120
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