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3FQR
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (148 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
:
1.70
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)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
6
Ligand/Ion
CADMIUM ION
2
GOL
3
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
[
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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
ARG A:6 , PHE A:8 , ASP A:29 , ASP A:30 , HOH A:336 , HOH A:507 , HOH A:516 , TYR B:62 , HOH B:273
BINDING SITE FOR RESIDUE GOL A 276
02
AC2
SOFTWARE
GLU A:19 , HOH A:607 , HIS B:12 , PRO B:13
BINDING SITE FOR RESIDUE MG A 277
03
AC3
SOFTWARE
GLY A:1 , HIS A:3 , HOH A:478 , HOH A:513
BINDING SITE FOR RESIDUE CD A 278
04
AC4
SOFTWARE
ASP A:30 , GLU A:212 , HOH A:301 , HOH A:309 , HOH A:551
BINDING SITE FOR RESIDUE CD A 279
05
AC5
SOFTWARE
HIS A:151 , GLU A:154 , HIS A:191 , HOH A:401
BINDING SITE FOR RESIDUE CD A 280
06
AC6
SOFTWARE
HIS A:145 , HIS A:197 , GLU A:198 , HOH A:407
BINDING SITE FOR RESIDUE CD A 281
07
AC7
SOFTWARE
SER B:32 , ASP B:33 , HOH B:113 , HOH B:154 , HOH B:338
BINDING SITE FOR RESIDUE GOL B 99
08
AC8
SOFTWARE
VAL A:231 , ARG A:234 , TRP A:244 , GLN B:7 , VAL B:8 , MET B:98 , HOH B:111 , HOH B:112
BINDING SITE FOR RESIDUE GOL B 100
09
AC9
SOFTWARE
ASN B:82 , HIS B:83 , LEU B:86 , HOH B:232 , HOH B:380
BINDING SITE FOR RESIDUE MG B 101
10
BC1
SOFTWARE
HIS B:50 , HOH B:103 , HOH B:133 , HOH B:261 , HOH B:409
BINDING SITE FOR RESIDUE CD B 102
11
BC2
SOFTWARE
ASP A:196 , SEP C:4 , HIS C:7 , HOH C:510
BINDING SITE FOR RESIDUE CD C 11
[
close Site info
]
SAPs(SNPs)/Variants
(36, 36)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_017614 (D3A, chain C, )
02: VAR_017615 (D3G, chain C, )
03: VAR_017616 (D3Y, chain C, )
04: VAR_017617 (S4F, chain C, )
05: VAR_017618 (S4L, chain C, )
06: VAR_017619 (S4Y, chain C, )
07: VAR_017620 (G5E, chain C, )
08: VAR_017621 (G5R, chain C, )
09: VAR_017622 (G5V, chain C, )
10: VAR_017623 (I6S, chain C, )
11: VAR_017624 (S8A, chain C, )
12: VAR_017625 (S8C, chain C, )
13: VAR_017626 (S8F, chain C, )
14: VAR_017627 (S8Y, chain C, )
15: VAR_004334 (F9Y, chain A, )
16: VAR_004335 (D30N, chain A, )
17: VAR_016726 (A41G, chain A, )
18: VAR_004336 (Q43R, chain A, )
19: VAR_004337 (K66N, chain A, )
20: VAR_016727 (H70Q, chain A, )
21: VAR_004338 (T73I, chain A, )
22: VAR_016728 (H74D, chain A, )
23: VAR_004339 (V95L, chain A, )
24: VAR_004340 (R97M, chain A, )
25: VAR_004341 (Y99C, chain A, )
26: VAR_004342 (Y99F, chain A, )
27: VAR_004343 (W107G, chain A, )
28: VAR_004344 (M138K, chain A, )
29: VAR_004345 (A149T, chain A, )
30: VAR_004346 (V152E, chain A, )
31: VAR_004348 (L156Q, chain A, )
32: VAR_004347 (L156W, chain A, )
33: VAR_004349 (T163E, chain A, )
34: VAR_016729 (E166D, chain A, )
35: VAR_016730 (W167G, chain A, )
36: VAR_004350 (A236E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_017614
D
32
A
CTNB1_HUMAN
Unclassified
---
C
D
3
A
02
UniProt
VAR_017615
D
32
G
CTNB1_HUMAN
Disease (PTR)
---
C
D
3
G
03
UniProt
VAR_017616
D
32
Y
CTNB1_HUMAN
Disease (PTR)
28931588
C
D
3
Y
04
UniProt
VAR_017617
S
33
F
CTNB1_HUMAN
Disease (PTR)
---
C
S
4
F
05
UniProt
VAR_017618
S
33
L
CTNB1_HUMAN
Unclassified
---
C
S
4
L
06
UniProt
VAR_017619
S
33
Y
CTNB1_HUMAN
Disease (PTR)
---
C
S
4
Y
07
UniProt
VAR_017620
G
34
E
CTNB1_HUMAN
Disease (PTR)
---
C
G
5
E
08
UniProt
VAR_017621
G
34
R
CTNB1_HUMAN
Unclassified
---
C
G
5
R
09
UniProt
VAR_017622
G
34
V
CTNB1_HUMAN
Polymorphism
28931589
C
G
5
V
10
UniProt
VAR_017623
I
35
S
CTNB1_HUMAN
Unclassified
---
C
I
6
S
11
UniProt
VAR_017624
S
37
A
CTNB1_HUMAN
Disease (MDB)
---
C
S
8
A
12
UniProt
VAR_017625
S
37
C
CTNB1_HUMAN
Disease (PTR)
---
C
S
8
C
13
UniProt
VAR_017626
S
37
F
CTNB1_HUMAN
Disease (PTR)
---
C
S
8
F
14
UniProt
VAR_017627
S
37
Y
CTNB1_HUMAN
Unclassified
---
C
S
8
Y
15
UniProt
VAR_004334
F
33
Y
1A02_HUMAN
Polymorphism
---
A
F
9
Y
16
UniProt
VAR_004335
D
54
N
1A02_HUMAN
Polymorphism
---
A
D
30
N
17
UniProt
VAR_016726
A
65
G
1A02_HUMAN
Polymorphism
---
A
A
41
G
18
UniProt
VAR_004336
Q
67
R
1A02_HUMAN
Polymorphism
---
A
Q
43
R
19
UniProt
VAR_004337
K
90
N
1A02_HUMAN
Polymorphism
---
A
K
66
N
20
UniProt
VAR_016727
H
94
Q
1A02_HUMAN
Polymorphism
---
A
H
70
Q
21
UniProt
VAR_004338
T
97
I
1A02_HUMAN
Polymorphism
---
A
T
73
I
22
UniProt
VAR_016728
H
98
D
1A02_HUMAN
Polymorphism
---
A
H
74
D
23
UniProt
VAR_004339
V
119
L
1A02_HUMAN
Polymorphism
---
A
V
95
L
24
UniProt
VAR_004340
R
121
M
1A02_HUMAN
Polymorphism
---
A
R
97
M
25
UniProt
VAR_004341
Y
123
C
1A02_HUMAN
Polymorphism
---
A
Y
99
C
26
UniProt
VAR_004342
Y
123
F
1A02_HUMAN
Polymorphism
---
A
Y
99
F
27
UniProt
VAR_004343
W
131
G
1A02_HUMAN
Polymorphism
---
A
W
107
G
28
UniProt
VAR_004344
M
162
K
1A02_HUMAN
Polymorphism
---
A
M
138
K
29
UniProt
VAR_004345
A
173
T
1A02_HUMAN
Polymorphism
---
A
A
149
T
30
UniProt
VAR_004346
V
176
E
1A02_HUMAN
Polymorphism
---
A
V
152
E
31
UniProt
VAR_004348
L
180
Q
1A02_HUMAN
Polymorphism
---
A
L
156
Q
32
UniProt
VAR_004347
L
180
W
1A02_HUMAN
Polymorphism
---
A
L
156
W
33
UniProt
VAR_004349
T
187
E
1A02_HUMAN
Polymorphism
---
A
T
163
E
34
UniProt
VAR_016729
E
190
D
1A02_HUMAN
Polymorphism
---
A
E
166
D
35
UniProt
VAR_016730
W
191
G
1A02_HUMAN
Polymorphism
---
A
W
167
G
36
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
[
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]
Exons
(1, 1)
Info
All Exons
Exon 1.9e (C:1-10)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.7/1.9e
2: Boundary 1.9e/1.10d
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
1.4e
ENST00000396185
4e
ENSE00001933873
chr3:
41240996-41241161
166
CTNB1_HUMAN
-
0
0
-
-
1.7
ENST00000396185
7
ENSE00002142861
chr3:
41265512-41265572
61
CTNB1_HUMAN
1-5
5
0
-
-
1.9e
ENST00000396185
9e
ENSE00001697426
chr3:
41266017-41266244
228
CTNB1_HUMAN
5-81
77
1
C:1-10
10
1.10d
ENST00000396185
10d
ENSE00001748344
chr3:
41266445-41266698
254
CTNB1_HUMAN
81-165
85
0
-
-
1.11b
ENST00000396185
11b
ENSE00001692569
chr3:
41266825-41267063
239
CTNB1_HUMAN
166-245
80
0
-
-
1.12
ENST00000396185
12
ENSE00001643204
chr3:
41267151-41267352
202
CTNB1_HUMAN
245-312
68
0
-
-
1.13
ENST00000396185
13
ENSE00001767208
chr3:
41268699-41268843
145
CTNB1_HUMAN
313-361
49
0
-
-
1.14
ENST00000396185
14
ENSE00001649367
chr3:
41274832-41274935
104
CTNB1_HUMAN
361-395
35
0
-
-
1.15
ENST00000396185
15
ENSE00001718373
chr3:
41275020-41275358
339
CTNB1_HUMAN
396-508
113
0
-
-
1.16a
ENST00000396185
16a
ENSE00001592339
chr3:
41275630-41275788
159
CTNB1_HUMAN
509-561
53
0
-
-
1.17b
ENST00000396185
17b
ENSE00001707050
chr3:
41277215-41277334
120
CTNB1_HUMAN
562-601
40
0
-
-
1.18a
ENST00000396185
18a
ENSE00002175036
chr3:
41277840-41277990
151
CTNB1_HUMAN
602-652
51
0
-
-
1.18d
ENST00000396185
18d
ENSE00001782706
chr3:
41278079-41278200
122
CTNB1_HUMAN
652-692
41
0
-
-
1.19
ENST00000396185
19
ENSE00001805633
chr3:
41279507-41279567
61
CTNB1_HUMAN
693-713
21
0
-
-
1.20c
ENST00000396185
20c
ENSE00001524181
chr3:
41280625-41280845
221
CTNB1_HUMAN
713-781
69
0
-
-
1.20g
ENST00000396185
20g
ENSE00001524178
chr3:
41281151-41281934
784
CTNB1_HUMAN
-
0
0
-
-
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3fqrb_ (B:)
View:
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Classes
(
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(
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Folds
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Protein Domains
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(
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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
d3fqrb_
B:
[
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_3fqrA01 (A:1-181)
2a: CATH_3fqrB00 (B:1-98)
2b: CATH_3fqrA02 (A:182-270)
View:
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Homologous Superfamilies
(
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(
)
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
3fqrA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
3fqrB00
B:1-98
2b
3fqrA02
A:182-270
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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