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3AY4
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (111 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NONFUCOSYLATED FC COMPLEXED WITH BIS-GLYCOSYLATED SOLUBLE FORM OF FC GAMMA RECEPTOR IIIA
Authors
:
T. Mizushima, E. Takemoto, H. Yagi, M. Shibata-Koyama, Y. Isoda, S. Iid M. Satoh, K. Kato
Date
:
28 Apr 11 (Deposition) - 03 Aug 11 (Release) - 09 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Immune System, Complex, Fc Fragment, Igg, Receptor, Cd16, Gamma
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Mizushima, H. Yagi, E. Takemoto, M. Shibata-Koyama, Y. Isoda, S. Iida, K. Masuda, M. Satoh, K. Kato
Structural Basis For Improved Efficacy Of Therapeutic Antibodies On Defucosylation Of Their Fc Glycans
Genes Cells V. 16 1071 2011
[
close entry info
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Hetero Components
(5, 27)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
2a: ALPHA-L-FUCOSE (FUCa)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
4
Ligand/Ion
BETA-D-MANNOSE
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
4
MAN
6
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
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Sites
(27, 27)
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)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:34 , HOH A:42 , HOH A:58 , ASP A:265 , GLN A:295 , ASN A:297 , NAG A:1002 , NAG C:1001 , NAG C:1002
BINDING SITE FOR RESIDUE NAG A 1001
02
AC2
SOFTWARE
HOH A:60 , PHE A:241 , ARG A:301 , NAG A:1001 , BMA A:1003 , MAN A:1007
BINDING SITE FOR RESIDUE NAG A 1002
03
AC3
SOFTWARE
PHE A:243 , NAG A:1002 , MAN A:1004 , MAN A:1007
BINDING SITE FOR RESIDUE BMA A 1003
04
AC4
SOFTWARE
BMA A:1003 , NAG A:1005
BINDING SITE FOR RESIDUE MAN A 1004
05
AC5
SOFTWARE
MAN A:1004
BINDING SITE FOR RESIDUE NAG A 1005
06
AC6
SOFTWARE
HOH A:182 , PHE A:243 , HOH A:456 , NAG A:1002 , BMA A:1003 , NAG A:1008 , MAN C:1004
BINDING SITE FOR RESIDUE MAN A 1007
07
AC7
SOFTWARE
PHE A:243 , LYS A:246 , THR A:260 , MAN A:1007 , GAL A:1009
BINDING SITE FOR RESIDUE NAG A 1008
08
AC8
SOFTWARE
HOH A:12 , PHE A:243 , PRO A:244 , PRO A:245 , LYS A:246 , GLU A:258 , THR A:260 , NAG A:1008
BINDING SITE FOR RESIDUE GAL A 1009
09
AC9
SOFTWARE
HOH B:160 , HOH B:203 , VAL B:264 , ASP B:265 , GLN B:295 , ASN B:297 , NAG B:1002
BINDING SITE FOR RESIDUE NAG B 1001
10
BC1
SOFTWARE
HOH B:168 , VAL B:264 , ARG B:301 , NAG B:1001 , BMA B:1003 , MAN B:1007
BINDING SITE FOR RESIDUE NAG B 1002
11
BC2
SOFTWARE
PHE B:243 , HOH B:460 , NAG B:1002 , MAN B:1004 , MAN B:1007
BINDING SITE FOR RESIDUE BMA B 1003
12
BC3
SOFTWARE
BMA B:1003 , NAG B:1005
BINDING SITE FOR RESIDUE MAN B 1004
13
BC4
SOFTWARE
MAN B:1004
BINDING SITE FOR RESIDUE NAG B 1005
14
BC5
SOFTWARE
PHE B:243 , NAG B:1002 , BMA B:1003 , NAG B:1008
BINDING SITE FOR RESIDUE MAN B 1007
15
BC6
SOFTWARE
HOH B:178 , PHE B:243 , THR B:260 , HOH B:468 , MAN B:1007 , GAL B:1009
BINDING SITE FOR RESIDUE NAG B 1008
16
BC7
SOFTWARE
PRO B:244 , LYS B:246 , GLU B:258 , THR B:260 , NAG B:1008
BINDING SITE FOR RESIDUE GAL B 1009
17
BC8
SOFTWARE
NAG A:1001 , LYS C:120 , ARG C:155 , LEU C:157 , ASN C:162 , HOH C:183 , HOH C:205 , HOH C:209 , NAG C:1002 , FUC C:1011
BINDING SITE FOR RESIDUE NAG C 1001
18
BC9
SOFTWARE
NAG A:1001 , ARG C:155 , HOH C:183 , HOH C:190 , HOH C:195 , NAG C:1001 , BMA C:1003 , FUC C:1011
BINDING SITE FOR RESIDUE NAG C 1002
19
CC1
SOFTWARE
TYR A:296 , NAG C:1002 , MAN C:1004 , MAN C:1007
BINDING SITE FOR RESIDUE BMA C 1003
20
CC2
SOFTWARE
MAN A:1007 , BMA C:1003 , NAG C:1005
BINDING SITE FOR RESIDUE MAN C 1004
21
CC3
SOFTWARE
MAN C:1004
BINDING SITE FOR RESIDUE NAG C 1005
22
CC4
SOFTWARE
TYR A:296 , BMA C:1003 , NAG C:1008
BINDING SITE FOR RESIDUE MAN C 1007
23
CC5
SOFTWARE
MAN C:1007
BINDING SITE FOR RESIDUE NAG C 1008
24
CC6
SOFTWARE
NAG C:1001 , NAG C:1002
BINDING SITE FOR RESIDUE FUC C 1011
25
CC7
SOFTWARE
HIS C:44 , ASN C:45 , ASP C:64 , SER C:66 , NAG C:1102
BINDING SITE FOR RESIDUE NAG C 1101
26
CC8
SOFTWARE
ASP C:64 , NAG C:1101 , BMA C:1103
BINDING SITE FOR RESIDUE NAG C 1102
27
CC9
SOFTWARE
NAG C:1102
BINDING SITE FOR RESIDUE BMA C 1103
[
close Site info
]
SAPs(SNPs)/Variants
(7, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_008800 (L48H, chain C, )
2: VAR_008799 (L48R, chain C, )
3: VAR_058398 (G129D, chain C, )
4: VAR_058399 (Y140H, chain C, )
5: VAR_003960 (V158V, chain C, )
6: VAR_003887 (D356E, chain A/B, )
7: VAR_003888 (L358M, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_008800
L
66
H
FCG3A_HUMAN
Disease (IMD20)
10127939
C
L
48
H
2
UniProt
VAR_008799
L
66
R
FCG3A_HUMAN
Polymorphism
10127939
C
L
48
R
3
UniProt
VAR_058398
G
147
D
FCG3A_HUMAN
Polymorphism
443082
C
G
129
D
4
UniProt
VAR_058399
Y
158
H
FCG3A_HUMAN
Polymorphism
396716
C
Y
140
H
5
UniProt
VAR_003960
F
176
V
FCG3A_HUMAN
Polymorphism
396991
C
V
158
V
6
UniProt
VAR_003887
D
239
E
IGHG1_HUMAN
Unclassified
---
A/B
D
356
E
7
UniProt
VAR_003888
L
241
M
IGHG1_HUMAN
Unclassified
---
A/B
L
358
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (-|A:423-429,B:423-429)
;
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.
IGHG1_HUMAN
81-87
306-312
2
-
A:423-429
B:423-429
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.2 (A:229-231 | B:229-231)
Exon 1.3b (A:231-341 | B:231-341)
Exon 1.4c (A:341-443 | B:341-444)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3b
3: Boundary 1.3b/1.4c
4: Boundary 1.4c/-
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
1.1
ENST00000390549
1
ENSE00001838294
chr14:
106209408-106209114
295
IGHG1_HUMAN
1-99
99
0
-
-
1.2
ENST00000390549
2
ENSE00001719055
chr14:
106208722-106208678
45
IGHG1_HUMAN
99-114
16
2
A:229-231
B:229-231
3
3
1.3b
ENST00000390549
3b
ENSE00001776617
chr14:
106208559-106208230
330
IGHG1_HUMAN
114-224
111
2
A:231-341
B:231-341
111
111
1.4c
ENST00000390549
4c
ENSE00001837466
chr14:
106208132-106207675
458
IGHG1_HUMAN
224-330
107
2
A:341-443
B:341-444
103
104
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3ay4a1 (A:229-341)
1b: SCOP_d3ay4b1 (B:229-341)
2a: SCOP_d3ay4a2 (A:342-443)
2b: SCOP_d3ay4b2 (B:342-444)
3a: SCOP_d3ay4c1 (C:5-86)
3b: SCOP_d3ay4c2 (C:87-174)
View:
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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
:
Immunoglobulin heavy chain gamma constant domain 2, CH2-gamma
(36)
Human (Homo sapiens) [TaxId: 9606]
(31)
1a
d3ay4a1
A:229-341
1b
d3ay4b1
B:229-341
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma
(38)
Human (Homo sapiens) [TaxId: 9606]
(31)
2a
d3ay4a2
A:342-443
2b
d3ay4b2
B:342-444
Family
:
I set domains
(152)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(22)
3a
d3ay4c1
C:5-86
3b
d3ay4c2
C:87-174
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
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