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2JG8
Asym. Unit
Info
Asym.Unit (142 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (69 KB)
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(1)
Title
:
CRYSTALLOGRAPHIC STRUCTURE OF HUMAN C1Q GLOBULAR HEADS COMPLEXED TO PHOSPHATIDYL-SERINE
Authors
:
H. Paidassi, P. Tacnet-Delorme, V. Garlatti, C. Darnault, B. Ghebrehiwet, C. Gaboriaud, G. J. Arlaud, P. Frachet
Date
:
09 Feb 07 (Deposition) - 19 Feb 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Polymorphism, Glycoprotein, Phagocytosis, Disease Mutation, Complement Pathway, Immune System, Cell Surface Molecule, Pyrrolidone Carboxylic Acid, Hydroxylation, Innate Immunity, Immune Response, Collagen, Tolerance, Apopotosis, Complement
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
H. Paidassi, P. Tacnet-Delorme, V. Garlatti, C. Darnault, B. Ghebrehiwet, C. Gaboriaud, G. J. Arlaud, P. Frachet
C1Q Binds Phosphatidylserine And Likely Acts As A Multiligand-Bridging Molecule In Apoptotic Cell Recognition.
J. Immunol. V. 180 2329 2008
[
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SEP
1
Mod. Residue
PHOSPHOSERINE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:112 , ASN A:124 , HIS A:125 , HOH A:2060
BINDING SITE FOR RESIDUE NAG A1223
2
AC2
SOFTWARE
GLN A:177 , ASP B:172 , TYR B:173 , GLN B:179 , HOH C:2044
BINDING SITE FOR RESIDUE CA B1224
3
AC3
SOFTWARE
GLN D:177 , ASP E:172 , TYR E:173 , GLN E:179 , HOH F:2044
BINDING SITE FOR RESIDUE CA E1224
4
AC4
SOFTWARE
LEU C:109 , SER C:126 , THR C:127 , GLN D:160 , VAL D:161 , ARG D:162
BINDING SITE FOR RESIDUE SEP D1223
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035551 (A96T, chain B/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_035551
A
123
T
C1QB_HUMAN
Unclassified
---
B/E
A
96
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: C1Q (C:87-217)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
C1Q
PS50871
C1q domain profile.
C1QC_HUMAN
115-245
1
C:87-217
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Exons
(3, 6)
Info
All Exons
Exon 1.5c (B:91-224 | E:92-224)
Exon 2.3b (C:87-217 | F:89-217)
Exon 3.4c (A:90-222 | D:90-222)
View:
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All Exon Boundaries
1: Boundary 1.4/1.5c
2: Boundary 1.5c/-
3: Boundary 2.2/2.3b
4: Boundary 2.3b/-
5: Boundary 3.3b/3.4c
6: Boundary 3.4c/-
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
1.2a
ENST00000314933
2a
ENSE00001464096
chr1:
22979474-22979796
323
C1QB_HUMAN
-
0
0
-
-
1.4
ENST00000314933
4
ENSE00001273267
chr1:
22985933-22986136
204
C1QB_HUMAN
1-63
63
0
-
-
1.5c
ENST00000314933
5c
ENSE00001210122
chr1:
22987305-22988031
727
C1QB_HUMAN
63-253
191
2
B:91-224
E:92-224
134
133
2.1a
ENST00000374640
1a
ENSE00001464107
chr1:
22970123-22970207
85
C1QC_HUMAN
-
0
0
-
-
2.2
ENST00000374640
2
ENSE00001464106
chr1:
22970504-22970697
194
C1QC_HUMAN
1-61
61
0
-
-
2.3b
ENST00000374640
3b
ENSE00001542062
chr1:
22973720-22974603
884
C1QC_HUMAN
61-245
185
2
C:87-217
F:89-217
131
129
3.1
ENST00000374642
1
ENSE00001413929
chr1:
22962999-22963195
197
C1QA_HUMAN
-
0
0
-
-
3.3b
ENST00000374642
3b
ENSE00001464114
chr1:
22964103-22964272
170
C1QA_HUMAN
1-55
55
0
-
-
3.4c
ENST00000374642
4c
ENSE00001548747
chr1:
22965326-22966101
776
C1QA_HUMAN
55-245
191
2
A:90-222
D:90-222
133
133
[
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SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2jg8a1 (A:90-222)
1b: SCOP_d2jg8d1 (D:90-222)
2a: SCOP_d2jg8b1 (B:92-223)
2b: SCOP_d2jg8e1 (E:92-223)
3a: SCOP_d2jg8c1 (C:89-217)
3b: SCOP_d2jg8f1 (F:89-217)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
Complement c1q globular head, A chain
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2jg8a1
A:90-222
1b
d2jg8d1
D:90-222
Protein domain
:
Complement c1q globular head, B chain
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d2jg8b1
B:92-223
2b
d2jg8e1
E:92-223
Protein domain
:
Complement c1q globular head, C chain
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
3a
d2jg8c1
C:89-217
3b
d2jg8f1
F:89-217
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2jg8A00 (A:90-222)
1b: CATH_2jg8B00 (B:91-224)
1c: CATH_2jg8E00 (E:92-224)
1d: CATH_2jg8C00 (C:87-217)
1e: CATH_2jg8F00 (F:89-217)
1f: CATH_2jg8D00 (D:90-222)
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)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.40, no name defined]
(56)
Human (Homo sapiens)
(38)
1a
2jg8A00
A:90-222
1b
2jg8B00
B:91-224
1c
2jg8E00
E:92-224
1d
2jg8C00
C:87-217
1e
2jg8F00
F:89-217
1f
2jg8D00
D:90-222
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_C1q_2jg8D01 (D:94-219)
1b: PFAM_C1q_2jg8D02 (D:94-219)
1c: PFAM_C1q_2jg8E01 (E:96-220)
1d: PFAM_C1q_2jg8E02 (E:96-220)
1e: PFAM_C1q_2jg8F01 (F:93-214)
1f: PFAM_C1q_2jg8F02 (F:93-214)
2a: PFAM_Collagen_2jg8B01 (B:91-93)
2b: PFAM_Collagen_2jg8C01 (C:87-89)
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Clans
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(
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(
)
Organisms
(
)
(
)
Clan
:
C1q_TNF
(45)
Family
:
C1q
(8)
Homo sapiens (Human)
(7)
1a
C1q-2jg8D01
D:94-219
1b
C1q-2jg8D02
D:94-219
1c
C1q-2jg8E01
E:96-220
1d
C1q-2jg8E02
E:96-220
1e
C1q-2jg8F01
F:93-214
1f
C1q-2jg8F02
F:93-214
Clan
:
no clan defined [family: Collagen]
(7)
Family
:
Collagen
(7)
Homo sapiens (Human)
(2)
2a
Collagen-2jg8B01
B:91-93
2b
Collagen-2jg8C01
C:87-89
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