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3FQU
Asym. Unit
Info
Asym.Unit (149 KB)
Biol.Unit 1 (143 KB)
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(1)
Title
:
PHOSPHORYLATION OF SELF-PEPTIDES ALTERS HUMAN LEUKOCYTE ANTIGEN CLASS I-RESTRICTED ANTIGEN PRESENTATION AND GENERATES TUMOR SPECIFIC EPITOPES
Authors
:
J. Petersen, J. Rossjohn
Date
:
07 Jan 09 (Deposition) - 03 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Immune System, Phosphorylation, Glycoprotein, Immune Response, Membrane, Mhc I, Phosphoprotein, Transmembrane, Disease Mutation, Immunoglobulin Domain, Pyrrolidone Carboxylic Acid, Secreted, Cancer, Tcr, Self-Epitope
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Petersen, S. J. Wurzbacher, N. A. Williamson, S. H. Ramarathinam, H. H. Reid, A. K. Nair, A. Y. Zhao, R. Nastovska, G. Rudge, J. Rossjohn, A. W. Purcell
Phosphorylated Self-Peptides Alter Human Leukocyte Antigen Class I-Restricted Antigen Presentation And Generate Tumor-Specific Epitopes
Proc. Natl. Acad. Sci. Usa V. 106 2776 2009
[
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
3a: MAGNESIUM ION (MGa)
4a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
6
Ligand/Ion
CADMIUM ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:58 , TYR A:59 , GLY A:62 , GLU A:63 , LYS A:66
BINDING SITE FOR RESIDUE GOL A 276
02
AC2
SOFTWARE
ARG A:6 , ASP A:29 , ASP A:30 , HOH A:400 , HOH A:402 , HOH A:509
BINDING SITE FOR RESIDUE GOL A 277
03
AC3
SOFTWARE
GLU A:166 , TRP A:167 , ARG A:170
BINDING SITE FOR RESIDUE GOL A 278
04
AC4
SOFTWARE
HIS A:145 , HIS A:197 , GLU A:198 , HOH A:361 , HOH A:377 , HOH A:398 , HOH A:425
BINDING SITE FOR RESIDUE CD A 279
05
AC5
SOFTWARE
HIS A:151 , GLU A:154 , HIS A:191 , CD A:283 , HOH A:363
BINDING SITE FOR RESIDUE CD A 280
06
AC6
SOFTWARE
GLY A:1 , HIS A:3 , HOH A:339 , HOH A:353
BINDING SITE FOR RESIDUE CD A 281
07
AC7
SOFTWARE
ASP A:30 , GLU A:212 , HOH A:480 , HOH A:532 , HOH A:556
BINDING SITE FOR RESIDUE CD A 282
08
AC8
SOFTWARE
HIS A:151 , GLU A:154 , CD A:280 , HOH A:354 , HOH A:546
BINDING SITE FOR RESIDUE CD A 283
09
AC9
SOFTWARE
GLU A:19 , GLN A:72 , HOH A:572 , HIS B:12 , PRO B:13
BINDING SITE FOR RESIDUE MG A 284
10
BC1
SOFTWARE
ILE A:23 , SER B:32 , ASP B:33 , HOH B:117 , HOH B:164 , HOH B:319
BINDING SITE FOR RESIDUE GOL B 99
11
BC2
SOFTWARE
HOH A:461 , HIS B:50 , HOH B:374 , HOH B:375 , HOH B:376
BINDING SITE FOR RESIDUE CD B 100
[
close Site info
]
SAPs(SNPs)/Variants
(22, 22)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004334 (F9Y, chain A, )
02: VAR_004335 (D30N, chain A, )
03: VAR_016726 (A41G, chain A, )
04: VAR_004336 (Q43R, chain A, )
05: VAR_004337 (K66N, chain A, )
06: VAR_016727 (H70Q, chain A, )
07: VAR_004338 (T73I, chain A, )
08: VAR_016728 (H74D, chain A, )
09: VAR_004339 (V95L, chain A, )
10: VAR_004340 (R97M, chain A, )
11: VAR_004341 (Y99C, chain A, )
12: VAR_004342 (Y99F, chain A, )
13: VAR_004343 (W107G, chain A, )
14: VAR_004344 (M138K, chain A, )
15: VAR_004345 (A149T, chain A, )
16: VAR_004346 (V152E, chain A, )
17: VAR_004348 (L156Q, chain A, )
18: VAR_004347 (L156W, chain A, )
19: VAR_004349 (T163E, chain A, )
20: VAR_016729 (E166D, chain A, )
21: VAR_016730 (W167G, chain A, )
22: VAR_004350 (A236E, chain A, )
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
F
9
Y
02
UniProt
VAR_004335
D
54
N
1A02_HUMAN
Polymorphism
---
A
D
30
N
03
UniProt
VAR_016726
A
65
G
1A02_HUMAN
Polymorphism
---
A
A
41
G
04
UniProt
VAR_004336
Q
67
R
1A02_HUMAN
Polymorphism
---
A
Q
43
R
05
UniProt
VAR_004337
K
90
N
1A02_HUMAN
Polymorphism
---
A
K
66
N
06
UniProt
VAR_016727
H
94
Q
1A02_HUMAN
Polymorphism
---
A
H
70
Q
07
UniProt
VAR_004338
T
97
I
1A02_HUMAN
Polymorphism
---
A
T
73
I
08
UniProt
VAR_016728
H
98
D
1A02_HUMAN
Polymorphism
---
A
H
74
D
09
UniProt
VAR_004339
V
119
L
1A02_HUMAN
Polymorphism
---
A
V
95
L
10
UniProt
VAR_004340
R
121
M
1A02_HUMAN
Polymorphism
---
A
R
97
M
11
UniProt
VAR_004341
Y
123
C
1A02_HUMAN
Polymorphism
---
A
Y
99
C
12
UniProt
VAR_004342
Y
123
F
1A02_HUMAN
Polymorphism
---
A
Y
99
F
13
UniProt
VAR_004343
W
131
G
1A02_HUMAN
Polymorphism
---
A
W
107
G
14
UniProt
VAR_004344
M
162
K
1A02_HUMAN
Polymorphism
---
A
M
138
K
15
UniProt
VAR_004345
A
173
T
1A02_HUMAN
Polymorphism
---
A
A
149
T
16
UniProt
VAR_004346
V
176
E
1A02_HUMAN
Polymorphism
---
A
V
152
E
17
UniProt
VAR_004348
L
180
Q
1A02_HUMAN
Polymorphism
---
A
L
156
Q
18
UniProt
VAR_004347
L
180
W
1A02_HUMAN
Polymorphism
---
A
L
156
W
19
UniProt
VAR_004349
T
187
E
1A02_HUMAN
Polymorphism
---
A
T
163
E
20
UniProt
VAR_016729
E
190
D
1A02_HUMAN
Polymorphism
---
A
E
166
D
21
UniProt
VAR_016730
W
191
G
1A02_HUMAN
Polymorphism
---
A
W
167
G
22
UniProt
VAR_004350
A
260
E
1A02_HUMAN
Polymorphism
---
A
A
236
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:77-83,A:257-263)
;
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
1
B:77-83
1A02_HUMAN
281-287
1
A:257-263
[
close PROSITE info
]
Exons
(1, 1)
Info
All Exons
Exon 1.1b (C:1-9)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.2a
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
1.1b
ENST00000245960
1b
ENSE00001353605
chr20:
3776482-3777378
897
MPIP2_HUMAN
1-67
67
1
C:1-9
9
1.2a
ENST00000245960
2a
ENSE00000858842
chr20:
3778269-3778396
128
MPIP2_HUMAN
67-110
44
0
-
-
1.3
ENST00000245960
3
ENSE00000858844
chr20:
3779059-3779110
52
MPIP2_HUMAN
110-127
18
0
-
-
1.4
ENST00000245960
4
ENSE00000858846
chr20:
3780935-3780976
42
MPIP2_HUMAN
127-141
15
0
-
-
1.5
ENST00000245960
5
ENSE00000858850
chr20:
3781109-3781145
37
MPIP2_HUMAN
141-153
13
0
-
-
1.6a
ENST00000245960
6a
ENSE00000657911
chr20:
3781390-3781512
123
MPIP2_HUMAN
154-194
41
0
-
-
1.6c
ENST00000245960
6c
ENSE00000858854
chr20:
3781618-3781740
123
MPIP2_HUMAN
195-235
41
0
-
-
1.7
ENST00000245960
7
ENSE00000657912
chr20:
3781901-3782035
135
MPIP2_HUMAN
236-280
45
0
-
-
1.8b
ENST00000245960
8b
ENSE00000858860
chr20:
3782369-3782449
81
MPIP2_HUMAN
281-307
27
0
-
-
1.9
ENST00000245960
9
ENSE00001482099
chr20:
3782571-3782747
177
MPIP2_HUMAN
308-366
59
0
-
-
1.10
ENST00000245960
10
ENSE00001190140
chr20:
3782928-3783023
96
MPIP2_HUMAN
367-398
32
0
-
-
1.11c
ENST00000245960
11c
ENSE00001658249
chr20:
3783557-3783619
63
MPIP2_HUMAN
399-419
21
0
-
-
1.12b
ENST00000245960
12b
ENSE00001645639
chr20:
3783755-3783853
99
MPIP2_HUMAN
420-452
33
0
-
-
1.13c
ENST00000245960
13c
ENSE00001714978
chr20:
3784051-3784184
134
MPIP2_HUMAN
453-497
45
0
-
-
1.14
ENST00000245960
14
ENSE00001664388
chr20:
3785216-3785327
112
MPIP2_HUMAN
497-534
38
0
-
-
1.15d
ENST00000245960
15d
ENSE00001869849
chr20:
3785468-3786762
1295
MPIP2_HUMAN
535-580
46
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3fqub_ (B:)
View:
Select:
Label:
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
d3fqub_
B:
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_3fquA01 (A:1-181)
2a: CATH_3fquB00 (B:1-98)
2b: CATH_3fquA02 (A:182-270)
View:
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Label:
Classes
(
)
(
)
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)
Human (Homo sapiens)
(249)
1a
3fquA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
3fquB00
B:1-98
2b
3fquA02
A:182-270
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
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Protein & NOT Site
Protein & NOT PROSITE
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Chain C
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Asym.Unit (149 KB)
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