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1ONQ
Asym. Unit
Info
Asym.Unit (146 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (68 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CD1A IN COMPLEX WITH A SULFATIDE
Authors
:
D. M. Zajonc, M. A. Elsliger, L. Teyton, I. A. Wilson
Date
:
28 Feb 03 (Deposition) - 05 Aug 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Protein-Glycolipid Complex, Beta Sheet Platform, , Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Zajonc, M. A. Elsliger, L. Teyton, I. A. Wilson
Crystal Structure Of Cd1A In Complex With A Sulfatide Self Antigen At A Resolution Of 2. 15 A.
Nat. Immunol. V. 4 808 2003
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
1b: ALPHA-L-FUCOSE (FUCb)
1c: ALPHA-L-FUCOSE (FUCc)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3a: SULFATE-3-D-GALACTOSYL-BETA-1-1-N-... (SLFa)
3b: SULFATE-3-D-GALACTOSYL-BETA-1-1-N-... (SLFb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
3
Ligand/Ion
ALPHA-L-FUCOSE
2
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SLF
2
Ligand/Ion
SULFATE-3-D-GALACTOSYL-BETA-1-1-N-STEAROYL-D-SPHINGOSINE
[
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Sites
(13, 13)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:57 , PHE A:58 , ARG A:168 , NAG A:502 , FUC A:531 , HOH A:667 , HOH A:740
BINDING SITE FOR RESIDUE NAG A 501
02
AC2
SOFTWARE
ARG A:168 , LEU A:171 , NAG A:501 , HOH A:740 , HOH A:763
BINDING SITE FOR RESIDUE NAG A 502
03
AC3
SOFTWARE
ASP A:175 , NAG A:501 , HOH A:664
BINDING SITE FOR RESIDUE FUC A 531
04
AC4
SOFTWARE
ASN A:20 , FUC A:512 , HOH A:729 , HOH A:745 , HOH A:755
BINDING SITE FOR RESIDUE NAG A 511
05
AC5
SOFTWARE
TRP A:23 , NAG A:511 , ASP B:34
BINDING SITE FOR RESIDUE FUC A 512
06
AC6
SOFTWARE
ASN A:128 , NAG A:522 , HOH A:612 , HOH A:650 , HOH A:715 , HOH A:815
BINDING SITE FOR RESIDUE NAG A 521
07
AC7
SOFTWARE
ASP A:175 , NAG A:521 , HOH A:683 , HOH A:813 , GLU B:74 , LYS B:75 , GLU B:77 , LYS B:94
BINDING SITE FOR RESIDUE NAG A 522
08
AC8
SOFTWARE
ASN C:57 , PHE C:58 , ARG C:168 , NAG C:502 , FUC C:532 , HOH C:690
BINDING SITE FOR RESIDUE NAG C 501
09
AC9
SOFTWARE
ARG C:168 , NAG C:501 , HOH C:675 , HOH C:676 , HOH C:701
BINDING SITE FOR RESIDUE NAG C 502
10
BC1
SOFTWARE
ASP C:175 , NAG C:501
BINDING SITE FOR RESIDUE FUC C 532
11
BC2
SOFTWARE
ASN C:128 , HOH C:644
BINDING SITE FOR RESIDUE NAG C 511
12
BC3
SOFTWARE
TRP A:14 , TRP A:63 , PHE A:70 , ILE A:72 , ARG A:73 , ARG A:76 , SER A:77 , ILE A:81 , LEU A:114 , LEU A:148 , GLU A:154 , THR A:158
BINDING SITE FOR RESIDUE SLF A 601
13
BC4
SOFTWARE
PHE C:10 , VAL C:12 , TRP C:14 , TRP C:63 , PHE C:70 , ARG C:73 , THR C:74 , SER C:77 , ILE C:81 , GLY C:100 , LEU C:114 , LEU C:116 , LEU C:148 , THR C:158
BINDING SITE FOR RESIDUE SLF C 602
[
close Site info
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_010209 (I13I, chain A/C, )
2: VAR_010210 (W51W, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_010209
T
30
I
CD1A_HUMAN
Polymorphism
2269714
A/C
I
13
I
2
UniProt
VAR_010210
C
68
W
CD1A_HUMAN
Polymorphism
2269715
A/C
W
51
W
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:78-84,D:78-84,B:78-84,D:78-84,B:...)
;
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_GORGO
98-104
2
B:78-84
D:78-84
B2MG_HUMAN
98-104
2
B:78-84
D:78-84
B2MG_PANTR
98-104
2
B:78-84
D:78-84
[
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]
Exons
(7, 14)
Info
All Exons
Exon 1.1a (B:1-3 | D:1-3)
Exon 1.2a (B:3-96 | D:3-96)
Exon 1.4 (B:96-99 | D:96-99)
Exon 2.2 (A:7-92 | C:7-92)
Exon 2.3 (A:92-185 | C:92-185)
Exon 2.4 (A:185-278 | C:185-278)
Exon 2.5 (A:278-280 | C:278-279)
View:
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Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.4
4: Boundary 1.4/1.5
5: Boundary 2.1/2.2
6: Boundary 2.2/2.3
7: Boundary 2.3/2.4
8: Boundary 2.4/2.5
9: Boundary 2.5/2.6
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
ENSPTRT00000012956
1a
ENSPTRE00000370636
chr15:
41860468-41860604
137
B2MG_PANTR
1-23
23
2
B:1-3
D:1-3
3
3
1.2a
ENSPTRT00000012956
2a
ENSPTRE00000238527
chr15:
41864413-41864691
279
B2MG_PANTR
23-116
94
2
B:3-96
D:3-96
94
94
1.4
ENSPTRT00000012956
4
ENSPTRE00000238528
chr15:
41865318-41865345
28
B2MG_PANTR
116-119
4
2
B:96-99
D:96-99
4
4
1.5
ENSPTRT00000012956
5
ENSPTRE00000070423
chr15:
41866598-41867140
543
B2MG_PANTR
-
0
0
-
-
2.1
ENST00000289429
1
ENSE00001446470
chr1:
158223927-158224517
591
CD1A_HUMAN
1-20
20
0
-
-
2.2
ENST00000289429
2
ENSE00001075814
chr1:
158224874-158225140
267
CD1A_HUMAN
20-109
90
2
A:7-92
C:7-92
86
86
2.3
ENST00000289429
3
ENSE00001039139
chr1:
158225794-158226072
279
CD1A_HUMAN
109-202
94
2
A:92-185
C:92-185
94
94
2.4
ENST00000289429
4
ENSE00001601429
chr1:
158226576-158226854
279
CD1A_HUMAN
202-295
94
2
A:185-278
C:185-278
94
94
2.5
ENST00000289429
5
ENSE00001039144
chr1:
158227211-158227301
91
CD1A_HUMAN
295-325
31
2
A:278-280
C:278-279
3
2
2.6
ENST00000289429
6
ENSE00001446468
chr1:
158227471-158228059
589
CD1A_HUMAN
325-327
3
0
-
-
[
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]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1onqb_ (B:)
1b: SCOP_d1onqd_ (D:)
2a: SCOP_d1onqa1 (A:184-280)
2b: SCOP_d1onqc1 (C:184-279)
3a: SCOP_d1onqa2 (A:7-183)
3b: SCOP_d1onqc2 (C:7-183)
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Superfamilies
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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
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d1onqb_
B:
1b
d1onqd_
D:
Protein domain
:
CD1, alpha-3 domain
(24)
Human (Homo sapiens), CD1a [TaxId: 9606]
(5)
2a
d1onqa1
A:184-280
2b
d1onqc1
C:184-279
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
:
CD1, alpha-1 and alpha-2 domains
(39)
Human (Homo sapiens), CD1a [TaxId: 9606]
(10)
3a
d1onqa2
A:7-183
3b
d1onqc2
C:7-183
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1onqA01 (A:7-182)
1b: CATH_1onqC01 (C:7-182)
2a: CATH_1onqB00 (B:1-99)
2b: CATH_1onqD00 (D:1-99)
2c: CATH_1onqA02 (A:183-278)
2d: CATH_1onqC02 (C:183-278)
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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)
Human (Homo sapiens)
(249)
1a
1onqA01
A:7-182
1b
1onqC01
C:7-182
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1onqB00
B:1-99
2b
1onqD00
D:1-99
2c
1onqA02
A:183-278
2d
1onqC02
C:183-278
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_C1_set_1onqD01 (D:11-92)
1b: PFAM_C1_set_1onqD02 (D:11-92)
1c: PFAM_C1_set_1onqC01 (C:193-274)
1d: PFAM_C1_set_1onqC02 (C:193-274)
2a: PFAM_MHC_I_1onqC03 (C:7-181)
2b: PFAM_MHC_I_1onqC04 (C:7-181)
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Clans
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1onqD01
D:11-92
1b
C1-set-1onqD02
D:11-92
1c
C1-set-1onqC01
C:193-274
1d
C1-set-1onqC02
C:193-274
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-1onqC03
C:7-181
2b
MHC_I-1onqC04
C:7-181
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