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3SGK
Asym. Unit
Info
Asym.Unit (218 KB)
Biol.Unit 1 (210 KB)
Biol.Unit 2 (210 KB)
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(1)
Title
:
UNIQUE CARBOHYDRATE/CARBOHYDRATE INTERACTIONS ARE REQUIRED FOR HIGH AFFINITY BINDING OF FCGIII AND ANTIBODIES LACKING CORE FUCOSE
Authors
:
C. Ferrara, S. Grau, C. Jaeger, P. Sondermann, P. Bruenker, I. Waldhaue M. Hennig, A. Ruf, A. C. Rufer, M. Stihle, P. Umana, J. Benz
Date
:
15 Jun 11 (Deposition) - 03 Aug 11 (Release) - 04 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Fc Receptor, Antibody, Afucosylation, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Ferrara, S. Grau, C. Jager, P. Sondermann, P. Brunker, I. Waldhauer M. Hennig, A. Ruf, A. C. Rufer, M. Stihle, P. Umana, J. Benz
Unique Carbohydrate-Carbohydrate Interactions Are Required For High Affinity Binding Between Fcgammariii And Antibodie Lacking Core Fucose.
Proc. Natl. Acad. Sci. Usa V. 108 12669 2011
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Hetero Components
(4, 27)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
2g: ALPHA-D-MANNOSE (MANg)
2h: ALPHA-D-MANNOSE (MANh)
2i: ALPHA-D-MANNOSE (MANi)
3a: MALONATE ION (MLIa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
MAN
9
Ligand/Ion
ALPHA-D-MANNOSE
3
MLI
1
Ligand/Ion
MALONATE ION
4
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:159 , HOH A:191 , ASP A:265 , GLN A:295 , ASN A:297 , THR A:299 , HOH A:452 , NAG A:1447 , TYR C:132 , NAG C:1445 , NAG C:1447
BINDING SITE FOR RESIDUE NAG A 1445
02
AC2
SOFTWARE
HOH A:77 , PHE A:241 , VAL A:264 , ARG A:301 , NAG A:1445 , BMA A:1448 , MAN A:1450
BINDING SITE FOR RESIDUE NAG A 1447
03
AC3
SOFTWARE
PHE A:241 , PHE A:243 , NAG A:1447 , MAN A:1450 , MAN A:1451 , NAG A:1454
BINDING SITE FOR RESIDUE BMA A 1448
04
AC4
SOFTWARE
NAG A:1447 , BMA A:1448 , NAG A:1453
BINDING SITE FOR RESIDUE MAN A 1450
05
AC5
SOFTWARE
HOH A:104 , HOH A:207 , LYS A:246 , MAN A:1450
BINDING SITE FOR RESIDUE NAG A 1453
06
AC6
SOFTWARE
HOH A:87 , PHE A:241 , BMA A:1448 , NAG A:1452
BINDING SITE FOR RESIDUE MAN A 1451
07
AC7
SOFTWARE
HOH A:87 , MAN A:1451 , NAG A:1454
BINDING SITE FOR RESIDUE NAG A 1452
08
AC8
SOFTWARE
LEU A:242 , PHE A:243 , BMA A:1448 , NAG A:1452
BINDING SITE FOR RESIDUE NAG A 1454
09
AC9
SOFTWARE
PHE B:241 , BMA B:1448 , NAG B:1452
BINDING SITE FOR RESIDUE MAN B 1451
10
BC1
SOFTWARE
HOH B:99 , VAL B:264 , ASP B:265 , GLN B:295 , ASN B:297 , NAG B:1447
BINDING SITE FOR RESIDUE NAG B 1445
11
BC2
SOFTWARE
PHE B:241 , ARG B:301 , HOH B:451 , NAG B:1445 , BMA B:1448 , MAN B:1450
BINDING SITE FOR RESIDUE NAG B 1447
12
BC3
SOFTWARE
PHE B:243 , NAG B:1447 , MAN B:1450 , MAN B:1451 , NAG B:1452 , NAG B:1454
BINDING SITE FOR RESIDUE BMA B 1448
13
BC4
SOFTWARE
HOH B:29 , NAG B:1447 , BMA B:1448 , NAG B:1453
BINDING SITE FOR RESIDUE MAN B 1450
14
BC5
SOFTWARE
BMA B:1448 , MAN B:1451 , NAG B:1454
BINDING SITE FOR RESIDUE NAG B 1452
15
BC6
SOFTWARE
HOH B:26 , LYS B:246 , MAN B:1450
BINDING SITE FOR RESIDUE NAG B 1453
16
BC7
SOFTWARE
BMA B:1448 , NAG B:1452
BINDING SITE FOR RESIDUE NAG B 1454
17
BC8
SOFTWARE
HOH A:98 , NAG A:1445 , LYS C:120 , ARG C:155 , LEU C:157 , ASN C:162 , HOH C:227 , HOH C:243 , NAG C:1447
BINDING SITE FOR RESIDUE NAG C 1445
18
BC9
SOFTWARE
HOH A:98 , NAG A:1445 , ARG C:155 , HOH C:231 , HOH C:255 , NAG C:1445 , BMA C:1470
BINDING SITE FOR RESIDUE NAG C 1447
19
CC1
SOFTWARE
TYR A:296 , NAG C:1447 , MAN C:1471 , MAN C:1475
BINDING SITE FOR RESIDUE BMA C 1470
20
CC2
SOFTWARE
HOH A:77 , HOH A:191 , HOH C:233 , HOH C:252 , BMA C:1470 , MAN C:1472
BINDING SITE FOR RESIDUE MAN C 1471
21
CC3
SOFTWARE
HOH A:191 , GLN A:295 , MAN C:1471
BINDING SITE FOR RESIDUE MAN C 1472
22
CC4
SOFTWARE
BMA C:1470 , MAN C:1476 , MAN C:1477
BINDING SITE FOR RESIDUE MAN C 1475
23
CC5
SOFTWARE
ASN B:315 , MAN C:1475
BINDING SITE FOR RESIDUE MAN C 1476
24
CC6
SOFTWARE
TYR A:296 , LYS B:340 , MAN C:1475
BINDING SITE FOR RESIDUE MAN C 1477
25
CC7
SOFTWARE
HIS C:44 , ASN C:45 , ASP C:64 , SER C:66 , HOH C:226 , NAG C:1461
BINDING SITE FOR RESIDUE NAG C 1460
26
CC8
SOFTWARE
ASP C:64 , HOH C:229 , HOH C:236 , NAG C:1460
BINDING SITE FOR RESIDUE NAG C 1461
27
CC9
SOFTWARE
LEU A:251 , MET A:252 , ILE A:253 , ASN A:434 , HIS A:435 , HOH A:453 , PHE C:43 , GLU C:46 , SER C:47 , LEU C:48
BINDING SITE FOR RESIDUE MLI A 1
[
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
(2, 4)
Info
All Exons
Exon 1.3b (A:236-341 | B:232-341)
Exon 1.4c (A:341-444 | B:341-443)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3b
2: Boundary 1.3b/1.4c
3: 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
0
-
-
1.3b
ENST00000390549
3b
ENSE00001776617
chr14:
106208559-106208230
330
IGHG1_HUMAN
114-224
111
2
A:236-341
B:232-341
106
110
1.4c
ENST00000390549
4c
ENSE00001837466
chr14:
106208132-106207675
458
IGHG1_HUMAN
224-330
107
2
A:341-444
B:341-443
104
103
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3sgka1 (A:236-341)
1b: SCOP_d3sgkb1 (B:232-341)
2a: SCOP_d3sgka2 (A:342-444)
2b: SCOP_d3sgkb2 (B:342-443)
3a: SCOP_d3sgkc1 (C:5-86)
3b: SCOP_d3sgkc2 (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
d3sgka1
A:236-341
1b
d3sgkb1
B:232-341
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma
(38)
Human (Homo sapiens) [TaxId: 9606]
(31)
2a
d3sgka2
A:342-444
2b
d3sgkb2
B:342-443
Family
:
I set domains
(152)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(22)
3a
d3sgkc1
C:5-86
3b
d3sgkc2
C:87-174
[
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]
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:
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Label:
Sorry, no Info available
[
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(currently selected atoms:
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Nucleic
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Protein & NOT PROSITE
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Chain C
Asymmetric Unit 1
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Asym.Unit (218 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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