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Getting 'Exon' information from database.
3BPL
Asym. Unit
Info
Asym.Unit (100 KB)
Biol.Unit 1 (94 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE IL4-IL4R-COMMON GAMMA TERNARY COMPLEX
Authors
:
K. C. Garcia
Date
:
18 Dec 07 (Deposition) - 05 Feb 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.93
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Il4, Il13, Receptor, Cytokine, B-Cell Activation, Glycoprotein, Growth Factor, Secreted, Immune Response, Membrane, Phosphoprotein, Transmembrane, Disease Mutation, Host-Virus Interaction, Scid, Cytokine-Receptor Complex, Cytokine-Cytokine Receptor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. L. Laporte, Z. S. Juo, J. Vaclavikova, L. A. Colf, X. Qi, N. M. Heller, A. D. Keegan, K. C. Garcia
Molecular And Structural Basis Of Cytokine Receptor Pleiotropy In The Interleukin-4/13 System.
Cell(Cambridge, Mass. ) V. 132 259 2008
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
2
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC6 (SOFTWARE)
6: AC7 (SOFTWARE)
7: AC8 (SOFTWARE)
8: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY B:102 , ASN B:103 , SER B:119 , NAG B:902 , HOH B:944 , HOH B:973 , HOH B:986
BINDING SITE FOR RESIDUE NAG B 901
2
AC3
SOFTWARE
NAG B:901 , HOH B:941 , HOH B:943 , HOH B:1000
BINDING SITE FOR RESIDUE NAG B 902
3
AC4
SOFTWARE
ASN B:184 , NAG B:912 , FUC B:913
BINDING SITE FOR RESIDUE NAG B 911
4
AC5
SOFTWARE
NAG B:911
BINDING SITE FOR RESIDUE NAG B 912
5
AC6
SOFTWARE
THR B:186 , NAG B:911
BINDING SITE FOR RESIDUE FUC B 913
6
AC7
SOFTWARE
PHE C:43 , TYR C:47 , ASN C:49 , LEU C:84 , HOH C:957
BINDING SITE FOR RESIDUE NAG C 921
7
AC8
SOFTWARE
THR C:61 , ASN C:62 , PHE C:85
BINDING SITE FOR RESIDUE NAG C 931
8
AC9
SOFTWARE
ASN C:137 , ASN C:153 , HOH C:949 , HOH C:954
BINDING SITE FOR RESIDUE NAG C 941
[
close Site info
]
SAPs(SNPs)/Variants
(34, 34)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_020392 (C3R, chain A, )
02: VAR_002669 (C40G, chain C, )
03: VAR_002670 (E46G, chain C, )
04: VAR_002671 (E46K, chain C, )
05: VAR_059302 (I50F, chain B, )
06: VAR_059303 (I50L, chain B, )
07: VAR_008034 (I50V, chain B, )
08: VAR_002672 (N62K, chain C, )
09: VAR_002673 (Y67C, chain C, )
10: VAR_002674 (Y83C, chain C, )
11: VAR_020611 (E87K, chain C, )
12: VAR_002675 (G92D, chain C, )
13: VAR_002676 (C93F, chain C, )
14: VAR_002677 (C93R, chain C, )
15: VAR_002678 (H101P, chain C, )
16: VAR_002679 (Y103N, chain C, )
17: VAR_002680 (Q122P, chain C, )
18: VAR_002681 (I131N, chain C, )
19: VAR_002682 (A134V, chain C, )
20: VAR_002683 (L140H, chain C, )
21: VAR_002684 (L150P, chain C, )
22: VAR_002685 (L150Q, chain C, )
23: VAR_002686 (C160R, chain C, )
24: VAR_002687 (L161S, chain C, )
25: VAR_002688 (R200C, chain C, )
26: VAR_002689 (R202W, chain C, )
27: VAR_002690 (R204C, chain C, )
28: VAR_002691 (R204H, chain C, )
29: VAR_002692 (F205C, chain C, )
30: VAR_002693 (L208P, chain C, )
31: VAR_002694 (C209Y, chain C, )
32: VAR_002695 (G210R, chain C, )
33: VAR_002697 (W218C, chain C, )
34: VAR_002698 (S219I, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_020392
C
27
R
IL4_HUMAN
Polymorphism
4986964
A
C
3
R
02
UniProt
VAR_002669
C
62
G
IL2RG_HUMAN
Disease (XSCID)
---
C
C
40
G
03
UniProt
VAR_002670
E
68
G
IL2RG_HUMAN
Disease (XSCID)
---
C
E
46
G
04
UniProt
VAR_002671
E
68
K
IL2RG_HUMAN
Disease (XSCID)
---
C
E
46
K
05
UniProt
VAR_059302
I
75
F
IL4RA_HUMAN
Polymorphism
1805010
B
I
50
F
06
UniProt
VAR_059303
I
75
L
IL4RA_HUMAN
Polymorphism
1805010
B
I
50
L
07
UniProt
VAR_008034
I
75
V
IL4RA_HUMAN
Polymorphism
1805010
B
I
50
V
08
UniProt
VAR_002672
N
84
K
IL2RG_HUMAN
Disease (XSCID)
---
C
N
62
K
09
UniProt
VAR_002673
Y
89
C
IL2RG_HUMAN
Disease (XSCID)
---
C
Y
67
C
10
UniProt
VAR_002674
Y
105
C
IL2RG_HUMAN
Disease (XSCID)
---
C
Y
83
C
11
UniProt
VAR_020611
E
109
K
IL2RG_HUMAN
Polymorphism
17875899
C
E
87
K
12
UniProt
VAR_002675
G
114
D
IL2RG_HUMAN
Disease (XSCID)
---
C
G
92
D
13
UniProt
VAR_002676
C
115
F
IL2RG_HUMAN
Disease (XSCID)
---
C
C
93
F
14
UniProt
VAR_002677
C
115
R
IL2RG_HUMAN
Disease (XSCID)
---
C
C
93
R
15
UniProt
VAR_002678
H
123
P
IL2RG_HUMAN
Disease (XSCID)
---
C
H
101
P
16
UniProt
VAR_002679
Y
125
N
IL2RG_HUMAN
Disease (XSCID)
---
C
Y
103
N
17
UniProt
VAR_002680
Q
144
P
IL2RG_HUMAN
Disease (XSCID)
---
C
Q
122
P
18
UniProt
VAR_002681
I
153
N
IL2RG_HUMAN
Disease (XSCID)
---
C
I
131
N
19
UniProt
VAR_002682
A
156
V
IL2RG_HUMAN
Disease (XSCID)
---
C
A
134
V
20
UniProt
VAR_002683
L
162
H
IL2RG_HUMAN
Disease (XSCID)
---
C
L
140
H
21
UniProt
VAR_002684
L
172
P
IL2RG_HUMAN
Disease (XSCID)
---
C
L
150
P
22
UniProt
VAR_002685
L
172
Q
IL2RG_HUMAN
Disease (XSCID)
---
C
L
150
Q
23
UniProt
VAR_002686
C
182
R
IL2RG_HUMAN
Disease (XSCID)
---
C
C
160
R
24
UniProt
VAR_002687
L
183
S
IL2RG_HUMAN
Disease (XSCID)
---
C
L
161
S
25
UniProt
VAR_002688
R
222
C
IL2RG_HUMAN
Disease (XCID)
---
C
R
200
C
26
UniProt
VAR_002689
R
224
W
IL2RG_HUMAN
Disease (XSCID)
---
C
R
202
W
27
UniProt
VAR_002690
R
226
C
IL2RG_HUMAN
Disease (XSCID)
---
C
R
204
C
28
UniProt
VAR_002691
R
226
H
IL2RG_HUMAN
Disease (XSCID)
---
C
R
204
H
29
UniProt
VAR_002692
F
227
C
IL2RG_HUMAN
Disease (XSCID)
---
C
F
205
C
30
UniProt
VAR_002693
L
230
P
IL2RG_HUMAN
Disease (XSCID)
---
C
L
208
P
31
UniProt
VAR_002694
C
231
Y
IL2RG_HUMAN
Disease (XSCID)
---
C
C
209
Y
32
UniProt
VAR_002695
G
232
R
IL2RG_HUMAN
Disease (XSCID)
---
C
G
210
R
33
UniProt
VAR_002697
W
240
C
IL2RG_HUMAN
Disease (XSCID)
---
C
W
218
C
34
UniProt
VAR_002698
S
241
I
IL2RG_HUMAN
Disease (XSCID)
---
C
S
219
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 5)
Info
All PROSITE Patterns/Profiles
1: INTERLEUKIN_4_13 (A:7-32)
2: FN3 (B:100-199,C:134-227)
3: HEMATOPO_REC_S_F1 (B:166-196,C:191-224)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTERLEUKIN_4_13
PS00838
Interleukins -4 and -13 signature.
IL4_HUMAN
31-56
1
A:7-32
2
FN3
PS50853
Fibronectin type-III domain profile.
IL4RA_HUMAN
125-224
1
B:100-199
IL2RG_HUMAN
156-253
1
C:134-227
3
HEMATOPO_REC_S_F1
PS01355
Short hematopoietin receptor family 1 signature.
IL4RA_HUMAN
191-221
1
B:166-196
IL2RG_HUMAN
213-246
1
C:191-224
[
close PROSITE info
]
Exons
(14, 14)
Info
All Exons
Exon 1.1a (A:3-21)
Exon 1.2b (A:22-37)
Exon 1.3b (A:38-96)
Exon 1.4b (A:97-128)
Exon 2.2j (C:34-68)
Exon 2.3b (C:68-130)
Exon 2.3e (C:130-176)
Exon 2.4a (C:177-227)
Exon 3.3b (B:-2--1)
Exon 3.5 (B:-1-45)
Exon 3.6 (B:45-96)
Exon 3.7 (B:96-146)
Exon 3.8 (B:147-199)
Exon 3.10 (B:199-199)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2b
03: Boundary 1.2b/1.3b
04: Boundary 1.3b/1.4b
05: Boundary 1.4b/-
06: Boundary 2.2a/2.2j
07: Boundary 2.2j/2.3b
08: Boundary 2.3b/2.3e
09: Boundary 2.3e/2.4a
10: Boundary 2.4a/2.5b
11: Boundary 3.2/3.3b
12: Boundary 3.3b/3.5
13: Boundary 3.5/3.6
14: Boundary 3.6/3.7
15: Boundary 3.7/3.8
16: Boundary 3.8/3.10
17: Boundary 3.10/3.11
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
ENST00000231449
1a
ENSE00001334422
chr5:
132009678-132009877
200
IL4_HUMAN
1-45
45
1
A:3-21
19
1.2b
ENST00000231449
2b
ENSE00000763068
chr5:
132010151-132010198
48
IL4_HUMAN
46-61
16
1
A:22-37
16
1.3b
ENST00000231449
3b
ENSE00000763067
chr5:
132015406-132015582
177
IL4_HUMAN
62-120
59
1
A:38-96
59
1.4b
ENST00000231449
4b
ENSE00000854399
chr5:
132018178-132018368
191
IL4_HUMAN
121-153
33
1
A:97-128
32
2.2a
ENST00000374202
2a
ENSE00000979104
X:70331481-70331275
207
IL2RG_HUMAN
1-39
39
0
-
-
2.2j
ENST00000374202
2j
ENSE00001762572
X:70330900-70330747
154
IL2RG_HUMAN
39-90
52
1
C:34-68
35
2.3b
ENST00000374202
3b
ENSE00001775873
X:70330538-70330354
185
IL2RG_HUMAN
90-152
63
1
C:68-130
63
2.3e
ENST00000374202
3e
ENSE00001729247
X:70330145-70330006
140
IL2RG_HUMAN
152-198
47
1
C:130-176
47
2.4a
ENST00000374202
4a
ENSE00001636586
X:70329240-70329078
163
IL2RG_HUMAN
199-253
55
1
C:177-227
51
2.5b
ENST00000374202
5b
ENSE00001782907
X:70328545-70328449
97
IL2RG_HUMAN
253-285
33
0
-
-
2.5d
ENST00000374202
5d
ENSE00001629003
X:70328196-70328127
70
IL2RG_HUMAN
285-308
24
0
-
-
2.5h
ENST00000374202
5h
ENSE00001462774
X:70327771-70327254
518
IL2RG_HUMAN
309-369
61
0
-
-
3.1c
ENST00000395762
1c
ENSE00001522740
chr16:
27325252-27325341
90
IL4RA_HUMAN
-
0
0
-
-
3.2
ENST00000395762
2
ENSE00001522738
chr16:
27341387-27341519
133
IL4RA_HUMAN
-
0
0
-
-
3.3b
ENST00000395762
3b
ENSE00001522737
chr16:
27351507-27351594
88
IL4RA_HUMAN
1-24
24
1
B:-2--1
2
3.5
ENST00000395762
5
ENSE00000681600
chr16:
27353442-27353580
139
IL4RA_HUMAN
24-70
47
1
B:-1-45
47
3.6
ENST00000395762
6
ENSE00000411237
chr16:
27356190-27356341
152
IL4RA_HUMAN
70-121
52
1
B:45-96
52
3.7
ENST00000395762
7
ENSE00000681616
chr16:
27357788-27357939
152
IL4RA_HUMAN
121-171
51
1
B:96-146
51
3.8
ENST00000395762
8
ENSE00000681622
chr16:
27363861-27364017
157
IL4RA_HUMAN
172-224
53
1
B:147-199
53
3.10
ENST00000395762
10
ENSE00000681627
chr16:
27367129-27367228
100
IL4RA_HUMAN
224-257
34
1
B:199-199
1
3.11
ENST00000395762
11
ENSE00000681633
chr16:
27370237-27370315
79
IL4RA_HUMAN
257-283
27
0
-
-
3.12
ENST00000395762
12
ENSE00000830176
chr16:
27372087-27372136
50
IL4RA_HUMAN
284-300
17
0
-
-
3.13b
ENST00000395762
13b
ENSE00001522736
chr16:
27373573-27376099
2527
IL4RA_HUMAN
300-825
526
0
-
-
[
close EXON info
]
SCOP Domains
(3, 5)
Info
All SCOP Domains
1a: SCOP_d3bpla_ (A:)
2a: SCOP_d3bplb1 (B:-2-96)
2b: SCOP_d3bplb2 (B:97-199)
3a: SCOP_d3bplc1 (C:34-129)
3b: SCOP_d3bplc2 (C:130-227)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
4-helical cytokines
(168)
Superfamily
:
4-helical cytokines
(168)
Family
:
Short-chain cytokines
(78)
Protein domain
:
Interleukin-4 (IL-4)
(16)
Human (Homo sapiens) [TaxId: 9606]
(16)
1a
d3bpla_
A:
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Fibronectin type III
(212)
Family
:
Fibronectin type III
(180)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(23)
2a
d3bplb1
B:-2-96
2b
d3bplb2
B:97-199
Protein domain
:
Cytokine receptor common gamma chain
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
3a
d3bplc1
C:34-129
3b
d3bplc2
C:130-227
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_3bplA00 (A:3-128)
2a: CATH_3bplB01 (B:-2-96)
2b: CATH_3bplB02 (B:97-199)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Growth Hormone; Chain: A;
(136)
Homologous Superfamily
:
[code=1.20.1250.10, no name defined]
(130)
Human (Homo sapiens)
(110)
1a
3bplA00
A:3-128
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
3bplB01
B:-2-96
2b
3bplB02
B:97-199
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
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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(selected part)
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by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
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by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
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by Charge
by Rainbow (Group)
by Custom Color
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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