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3D5O
Asym. Unit
Info
Asym.Unit (203 KB)
Biol.Unit 1 (197 KB)
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(1)
Title
:
STRUCTURAL RECOGNITION AND FUNCTIONAL ACTIVATION OF FCRR BY INNATE PENTRAXINS
Authors
:
J. Lu, L. L. Marnell, K. D. Marjon, C. Mold, T. W. Du Clos, P. D. Sun
Date
:
16 May 08 (Deposition) - 11 Nov 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Complex Structure, Sap, Fc Riia, Fc Receptor Activation, Pentraxins, Amyloid, Glycoprotein, Lectin, Metal-Binding, Secreted, Cell Membrane, Igg-Binding Protein, Immunoglobulin Domain, Membrane, Phosphoprotein, Receptor, Transmembrane, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Lu, L. L. Marnell, K. D. Marjon, C. Mold, T. W. Du Clos, P. D. Sun
Structural Recognition And Functional Activation Of Fcgamma By Innate Pentraxins.
Nature V. 456 989 2008
[
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Hetero Components
(3, 22)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
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)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SO4
16
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:78 , ARG A:120 , GLN A:121
BINDING SITE FOR RESIDUE SO4 A 205
02
AC2
SOFTWARE
HIS A:19 , ASN A:21 , ARG A:193
BINDING SITE FOR RESIDUE SO4 A 206
03
AC3
SOFTWARE
LEU A:43 , SER A:44 , ARG A:45 , LYS B:83
BINDING SITE FOR RESIDUE SO4 A 207
04
AC4
SOFTWARE
HIS B:78 , LEU B:119 , ARG B:120
BINDING SITE FOR RESIDUE SO4 B 205
05
AC5
SOFTWARE
HIS B:19 , ASN B:21 , LYS B:130 , ARG B:193 , PRO F:2 , GLN F:69 , SER F:74 , LEU F:75
BINDING SITE FOR RESIDUE SO4 B 206
06
AC6
SOFTWARE
ASP B:42 , LEU B:43 , SER B:44 , ARG B:45 , LYS C:83
BINDING SITE FOR RESIDUE SO4 B 207
07
AC7
SOFTWARE
LEU C:119 , ARG C:120 , HOH C:213
BINDING SITE FOR RESIDUE SO4 C 205
08
AC8
SOFTWARE
HIS C:19 , ASN C:21 , ARG C:193
BINDING SITE FOR RESIDUE SO4 C 206
09
AC9
SOFTWARE
LEU C:43 , SER C:44 , ARG C:45 , LYS D:83
BINDING SITE FOR RESIDUE SO4 C 207
10
BC1
SOFTWARE
HIS D:78 , LEU D:119 , ARG D:120
BINDING SITE FOR RESIDUE SO4 D 205
11
BC2
SOFTWARE
HIS D:19 , ASN D:21 , GLY D:141 , ARG D:193
BINDING SITE FOR RESIDUE SO4 D 206
12
BC3
SOFTWARE
ASP D:42 , LEU D:43 , SER D:44 , ARG D:45 , LYS E:83
BINDING SITE FOR RESIDUE SO4 D 207
13
BC4
SOFTWARE
HIS E:78 , LEU E:119 , ARG E:120
BINDING SITE FOR RESIDUE SO4 E 205
14
BC5
SOFTWARE
HIS E:19 , ASN E:21 , ARG E:193
BINDING SITE FOR RESIDUE SO4 E 206
15
BC6
SOFTWARE
LYS A:83 , LEU E:43 , SER E:44 , ARG E:45
BINDING SITE FOR RESIDUE SO4 E 207
16
BC7
SOFTWARE
HIS F:94 , LEU F:95 , GLU F:96
BINDING SITE FOR RESIDUE SO4 F 178
17
BC8
SOFTWARE
ARG A:38 , PRO A:91 , ASN A:110 , TRP A:203 , SER F:34 , ASP F:35
BINDING SITE FOR RESIDUE GOL F 179
18
BC9
SOFTWARE
ASN A:32 , GLU A:99
BINDING SITE FOR RESIDUE NAG A 208
19
CC1
SOFTWARE
PRO A:25 , GLN B:31 , ASN B:32 , GLU B:99
BINDING SITE FOR RESIDUE NAG B 208
20
CC2
SOFTWARE
GLN C:31 , ASN C:32 , GLU C:99
BINDING SITE FOR RESIDUE NAG C 208
21
CC3
SOFTWARE
GLN D:31 , ASN D:32
BINDING SITE FOR RESIDUE NAG D 208
22
CC4
SOFTWARE
GLN E:31 , ASN E:32 , HOH E:209
BINDING SITE FOR RESIDUE NAG E 208
[
close Site info
]
SAPs(SNPs)/Variants
(6, 18)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_054857 (Q27R, chain F, )
2: VAR_054858 (M104V, chain F, )
3: VAR_035814 (G122S, chain A/B/C/D/E, )
4: VAR_003955 (R131R, chain F, )
5: VAR_006054 (E136G, chain A/B/C/D/E, )
6: VAR_006055 (S139G, chain A/B/C/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_054857
Q
63
R
FCG2A_HUMAN
Polymorphism
9427398
F
Q
27
R
2
UniProt
VAR_054858
M
140
V
FCG2A_HUMAN
Polymorphism
4986941
F
M
104
V
3
UniProt
VAR_035814
G
141
S
SAMP_HUMAN
Unclassified
---
A/B/C/D/E
G
122
S
4
UniProt
VAR_003955
H
167
R
FCG2A_HUMAN
Polymorphism
1801274
F
R
131
R
5
UniProt
VAR_006054
E
155
G
SAMP_HUMAN
Polymorphism
---
A/B/C/D/E
E
136
G
6
UniProt
VAR_006055
S
158
G
SAMP_HUMAN
Polymorphism
---
A/B/C/D/E
S
139
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 10)
Info
All PROSITE Patterns/Profiles
1: PTX_2 (A:5-204,B:5-204,C:5-204,D:5-204,E:...)
2: PTX_1 (A:93-100,B:93-100,C:93-100,D:93-10...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PTX_2
PS51828
Pentraxin (PTX) domain profile.
SAMP_HUMAN
24-223
5
A:5-204
B:5-204
C:5-204
D:5-204
E:5-204
2
PTX_1
PS00289
Pentraxin domain signature.
SAMP_HUMAN
112-119
5
A:93-100
B:93-100
C:93-100
D:93-100
E:93-100
[
close PROSITE info
]
Exons
(5, 13)
Info
All Exons
Exon 1.1 (A:1-3 | B:1-3 | C:1-3 | D:1-3 | E:...)
Exon 1.2 (A:3-204 | B:3-204 | C:3-204 | D:3-...)
Exon 2.1j (F:1-86)
Exon 2.3a (F:86-171)
Exon 2.4a (F:171-171)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/-
4: Boundary 2.1g/2.1j
5: Boundary 2.1j/2.3a
6: Boundary 2.3a/2.4a
7: Boundary 2.4a/2.6a
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
1.1
ENST00000255040
1
ENSE00000904938
chr1:
159557615-159557775
161
SAMP_HUMAN
1-22
22
5
A:1-3
B:1-3
C:1-3
D:1-3
E:1-3
3
3
3
3
3
1.2
ENST00000255040
2
ENSE00000904939
chr1:
159557891-159558655
765
SAMP_HUMAN
22-223
202
5
A:3-204
B:3-204
C:3-204
D:3-204
E:3-204
202
202
202
202
202
2.1a
ENST00000271450
1a
ENSE00001170978
chr1:
161475220-161475342
123
FCG2A_HUMAN
1-29
29
0
-
-
2.1g
ENST00000271450
1g
ENSE00000958752
chr1:
161475777-161475797
21
FCG2A_HUMAN
29-36
8
0
-
-
2.1j
ENST00000271450
1j
ENSE00001651726
chr1:
161476124-161476381
258
FCG2A_HUMAN
36-122
87
1
F:1-86
86
2.3a
ENST00000271450
3a
ENSE00001614571
chr1:
161479610-161479864
255
FCG2A_HUMAN
122-207
86
1
F:86-171
86
2.4a
ENST00000271450
4a
ENSE00000958755
chr1:
161480624-161480746
123
FCG2A_HUMAN
207-248
42
1
F:171-171
1
2.6a
ENST00000271450
6a
ENSE00001643425
chr1:
161483685-161483722
38
FCG2A_HUMAN
248-260
13
0
-
-
2.8h
ENST00000271450
8h
ENSE00001170974
chr1:
161487765-161489358
1594
FCG2A_HUMAN
261-317
57
0
-
-
[
close EXON info
]
SCOP Domains
(2, 7)
Info
All SCOP Domains
1a: SCOP_d3d5oa_ (A:)
1b: SCOP_d3d5ob_ (B:)
1c: SCOP_d3d5oc_ (C:)
1d: SCOP_d3d5od_ (D:)
1e: SCOP_d3d5oe_ (E:)
2a: SCOP_d3d5of1 (F:1-85)
2b: SCOP_d3d5of2 (F:86-171)
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Folds
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Pentraxin (pentaxin)
(18)
Protein domain
:
Serum amyloid P component (SAP)
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d3d5oa_
A:
1b
d3d5ob_
B:
1c
d3d5oc_
C:
1d
d3d5od_
D:
1e
d3d5oe_
E:
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
I set domains
(152)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(22)
2a
d3d5of1
F:1-85
2b
d3d5of2
F:86-171
[
close SCOP info
]
CATH Domains
(2, 7)
Info
all CATH domains
1a: CATH_3d5oF02 (F:87-171)
1b: CATH_3d5oF01 (F:1-86)
2a: CATH_3d5oA00 (A:1-204)
2b: CATH_3d5oB00 (B:1-204)
2c: CATH_3d5oC00 (C:1-204)
2d: CATH_3d5oD00 (D:1-204)
2e: CATH_3d5oE00 (E:1-204)
View:
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Architectures
(
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
3d5oF02
F:87-171
1b
3d5oF01
F:1-86
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Human (Homo sapiens)
(49)
2a
3d5oA00
A:1-204
2b
3d5oB00
B:1-204
2c
3d5oC00
C:1-204
2d
3d5oD00
D:1-204
2e
3d5oE00
E:1-204
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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Asym.Unit (203 KB)
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