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Getting 'Exon' information from database.
3OED
Asym. Unit
Info
Asym.Unit (280 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (139 KB)
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(1)
Title
:
THE STRUCTURE OF THE COMPLEX BETWEEN COMPLEMENT RECEPTOR CR2 AND ITS LIGAND COMPLEMENT FRAGMENT C3D
Authors
:
D. E. Isenman, J. M. H. Van Den Elsen
Date
:
12 Aug 10 (Deposition) - 11 May 11 (Release) - 28 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.16
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Complement Receptor, Complement Fragment C3D, B Cell, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Van Den Elsen, D. E. Isenman
A Crystal Structure Of The Complex Between Human Complement Receptor 2 And Its Ligand C3D.
Science V. 332 608 2011
[
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Hetero Components
(0, 0)
Info
All Hetero Components
View:
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Label:
Sorry, no Info available
[
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]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(7, 14)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_063655 (R49L, chain A/B, )
2: VAR_063216 (A101V, chain A/B, )
3: VAR_063217 (D122N, chain A/B, )
4: VAR_063218 (C165W, chain A/B, )
5: VAR_063219 (Q168K, chain A/B, )
6: VAR_022761 (D223N, chain A/B, )
7: VAR_019207 (G231D, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_063655
R
1042
L
CO3_HUMAN
Disease (AHUS5)
---
A/B
R
49
L
2
UniProt
VAR_063216
A
1094
V
CO3_HUMAN
Disease (AHUS5)
---
A/B
A
101
V
3
UniProt
VAR_063217
D
1115
N
CO3_HUMAN
Disease (AHUS5)
---
A/B
D
122
N
4
UniProt
VAR_063218
C
1158
W
CO3_HUMAN
Disease (AHUS5)
---
A/B
C
165
W
5
UniProt
VAR_063219
Q
1161
K
CO3_HUMAN
Disease (AHUS5)
---
A/B
Q
168
K
6
UniProt
VAR_022761
D
1216
N
CO3_HUMAN
Unclassified
---
A/B
D
223
N
7
UniProt
VAR_019207
G
1224
D
CO3_HUMAN
Polymorphism
11569534
A/B
G
231
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: SUSHI (C:1-64,D:1-64|C:69-128,D:69-128|-|...)
2: ALPHA_2_MACROGLOBULIN (A:14-22,B:14-22)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUSHI
PS50923
Sushi/CCP/SCR domain profile.
CR2_HUMAN
21-84
89-148
152-212
213-273
274-344
408-468
349-407
469-524
525-595
600-659
660-716
717-781
786-845
849-909
910-970
4
C:1-64
D:1-64
C:69-128
D:69-128
-
-
-
-
-
-
-
-
-
-
-
-
-
2
ALPHA_2_MACROGLOBULIN
PS00477
Alpha-2-macroglobulin family thiolester region signature.
CO3_HUMAN
1007-1015
2
A:14-22
B:14-22
[
close PROSITE info
]
Exons
(10, 20)
Info
All Exons
Exon 1.26 (A:1-59 | B:1-59)
Exon 1.27 (A:59-84 | B:59-84)
Exon 1.28c (A:84-137 | B:84-137)
Exon 1.29 (A:138-170 | B:138-170)
Exon 1.31a (A:171-223 | B:171-223)
Exon 1.31d (A:223-277 | B:223-277)
Exon 1.32 (A:278-294 | B:278-294)
Exon 2.1a (C:0-0 | D:0-0)
Exon 2.3b (C:0-129 | D:0-129)
Exon 2.4b (C:129-129 | D:129-129)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.25/1.26
02: Boundary 1.26/1.27
03: Boundary 1.27/1.28c
04: Boundary 1.28c/1.29
05: Boundary 1.29/1.31a
06: Boundary 1.31a/1.31d
07: Boundary 1.31d/1.32
08: Boundary 1.32/1.33
09: Boundary -/2.1a
10: Boundary 2.1a/2.3b
11: Boundary 2.3b/2.4b
12: Boundary 2.4b/2.5
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
1.3a
ENST00000245907
3a
ENSE00001938285
chr19:
6720693-6720527
167
CO3_HUMAN
1-25
25
0
-
-
1.4
ENST00000245907
4
ENSE00001053574
chr19:
6719414-6719222
193
CO3_HUMAN
25-89
65
0
-
-
1.5
ENST00000245907
5
ENSE00000858140
chr19:
6718423-6718258
166
CO3_HUMAN
90-145
56
0
-
-
1.6a
ENST00000245907
6a
ENSE00001053592
chr19:
6718175-6718105
71
CO3_HUMAN
145-168
24
0
-
-
1.7
ENST00000245907
7
ENSE00000858137
chr19:
6714457-6714363
95
CO3_HUMAN
169-200
32
0
-
-
1.8b
ENST00000245907
8b
ENSE00001053577
chr19:
6714259-6714177
83
CO3_HUMAN
200-228
29
0
-
-
1.9
ENST00000245907
9
ENSE00001053565
chr19:
6714093-6714003
91
CO3_HUMAN
228-258
31
0
-
-
1.11
ENST00000245907
11
ENSE00001053527
chr19:
6713520-6713418
103
CO3_HUMAN
258-292
35
0
-
-
1.12b
ENST00000245907
12b
ENSE00000858133
chr19:
6713326-6713200
127
CO3_HUMAN
293-335
43
0
-
-
1.13
ENST00000245907
13
ENSE00001053519
chr19:
6712634-6712519
116
CO3_HUMAN
335-373
39
0
-
-
1.14b
ENST00000245907
14b
ENSE00001053582
chr19:
6712417-6712268
150
CO3_HUMAN
374-423
50
0
-
-
1.15
ENST00000245907
15
ENSE00000858130
chr19:
6711207-6710998
210
CO3_HUMAN
424-493
70
0
-
-
1.16b
ENST00000245907
16b
ENSE00001159750
chr19:
6710856-6710650
207
CO3_HUMAN
494-562
69
0
-
-
1.17b
ENST00000245907
17b
ENSE00000858128
chr19:
6709853-6709695
159
CO3_HUMAN
563-615
53
0
-
-
1.18
ENST00000245907
18
ENSE00000858127
chr19:
6707940-6707811
130
CO3_HUMAN
616-659
44
0
-
-
1.19
ENST00000245907
19
ENSE00001053520
chr19:
6707548-6707477
72
CO3_HUMAN
659-683
25
0
-
-
1.20
ENST00000245907
20
ENSE00001053532
chr19:
6707284-6707087
198
CO3_HUMAN
683-749
67
0
-
-
1.21c
ENST00000245907
21c
ENSE00001053537
chr19:
6702590-6702482
109
CO3_HUMAN
749-785
37
0
-
-
1.22
ENST00000245907
22
ENSE00001053579
chr19:
6702223-6702138
86
CO3_HUMAN
785-814
30
0
-
-
1.23b
ENST00000245907
23b
ENSE00001053525
chr19:
6697805-6697663
143
CO3_HUMAN
814-861
48
0
-
-
1.23d
ENST00000245907
23d
ENSE00000858122
chr19:
6697567-6697355
213
CO3_HUMAN
862-932
71
0
-
-
1.24b
ENST00000245907
24b
ENSE00000858121
chr19:
6696670-6696604
67
CO3_HUMAN
933-955
23
0
-
-
1.25
ENST00000245907
25
ENSE00001053553
chr19:
6696476-6696390
87
CO3_HUMAN
955-984
30
0
-
-
1.26
ENST00000245907
26
ENSE00000858119
chr19:
6694645-6694442
204
CO3_HUMAN
984-1052
69
2
A:1-59
B:1-59
59
59
1.27
ENST00000245907
27
ENSE00000858118
chr19:
6693498-6693423
76
CO3_HUMAN
1052-1077
26
2
A:59-84
B:59-84
26
26
1.28c
ENST00000245907
28c
ENSE00000858117
chr19:
6693094-6692935
160
CO3_HUMAN
1077-1130
54
2
A:84-137
B:84-137
54
54
1.29
ENST00000245907
29
ENSE00000858116
chr19:
6690738-6690640
99
CO3_HUMAN
1131-1163
33
2
A:138-170
B:138-170
33
33
1.31a
ENST00000245907
31a
ENSE00000858115
chr19:
6686913-6686757
157
CO3_HUMAN
1164-1216
53
2
A:171-223
B:171-223
53
53
1.31d
ENST00000245907
31d
ENSE00001504968
chr19:
6686298-6686135
164
CO3_HUMAN
1216-1270
55
2
A:223-277
B:223-277
55
55
1.32
ENST00000245907
32
ENSE00001159688
chr19:
6685157-6684999
159
CO3_HUMAN
1271-1323
53
2
A:278-294
B:278-294
17
17
1.33
ENST00000245907
33
ENSE00000858111
chr19:
6684845-6684786
60
CO3_HUMAN
1324-1343
20
0
-
-
1.34a
ENST00000245907
34a
ENSE00001053551
chr19:
6684661-6684571
91
CO3_HUMAN
1344-1374
31
0
-
-
1.35a
ENST00000245907
35a
ENSE00000858109
chr19:
6684450-6684399
52
CO3_HUMAN
1374-1391
18
0
-
-
1.36b
ENST00000245907
36b
ENSE00000858108
chr19:
6682240-6682153
88
CO3_HUMAN
1391-1420
30
0
-
-
1.37
ENST00000245907
37
ENSE00000858107
chr19:
6682041-6681952
90
CO3_HUMAN
1421-1450
30
0
-
-
1.38
ENST00000245907
38
ENSE00000858106
chr19:
6680274-6680169
106
CO3_HUMAN
1451-1486
36
0
-
-
1.40a
ENST00000245907
40a
ENSE00000858105
chr19:
6679507-6679418
90
CO3_HUMAN
1486-1516
31
0
-
-
1.41a
ENST00000245907
41a
ENSE00000858104
chr19:
6679219-6679136
84
CO3_HUMAN
1516-1544
29
0
-
-
1.42
ENST00000245907
42
ENSE00000858103
chr19:
6678466-6678383
84
CO3_HUMAN
1544-1572
29
0
-
-
1.43
ENST00000245907
43
ENSE00000858102
chr19:
6678298-6678163
136
CO3_HUMAN
1572-1617
46
0
-
-
1.44c
ENST00000245907
44c
ENSE00001159829
chr19:
6678034-6677846
189
CO3_HUMAN
1617-1663
47
0
-
-
2.1a
ENST00000367058
1a
ENSE00001952555
chr1:
207627575-207627821
247
CR2_HUMAN
1-20
20
2
C:0-0
D:0-0
1
1
2.3b
ENST00000367058
3b
ENSE00001069650
chr1:
207639871-207640257
387
CR2_HUMAN
20-149
130
2
C:0-129
D:0-129
130
130
2.4b
ENST00000367058
4b
ENSE00000882434
chr1:
207641872-207642060
189
CR2_HUMAN
149-212
64
2
C:129-129
D:129-129
1
1
2.5
ENST00000367058
5
ENSE00000882436
chr1:
207642145-207642244
100
CR2_HUMAN
212-245
34
0
-
-
2.6
ENST00000367058
6
ENSE00000791926
chr1:
207642495-207642577
83
CR2_HUMAN
245-273
29
0
-
-
2.7b
ENST00000367058
7b
ENSE00000882439
chr1:
207643040-207643447
408
CR2_HUMAN
273-409
137
0
-
-
2.8
ENST00000367058
8
ENSE00000882440
chr1:
207644085-207644261
177
CR2_HUMAN
409-468
60
0
-
-
2.9a
ENST00000367058
9a
ENSE00000882441
chr1:
207644342-207644432
91
CR2_HUMAN
468-498
31
0
-
-
2.10
ENST00000367058
10
ENSE00001167936
chr1:
207644768-207644844
77
CR2_HUMAN
498-524
27
0
-
-
2.12b
ENST00000367058
12b
ENSE00001381764
chr1:
207646117-207646524
408
CR2_HUMAN
524-660
137
0
-
-
2.14
ENST00000367058
14
ENSE00001167916
chr1:
207647146-207647230
85
CR2_HUMAN
660-688
29
0
-
-
2.15
ENST00000367058
15
ENSE00001167908
chr1:
207647586-207647668
83
CR2_HUMAN
688-716
29
0
-
-
2.16a
ENST00000367058
16a
ENSE00001167899
chr1:
207648169-207648561
393
CR2_HUMAN
716-847
132
0
-
-
2.17
ENST00000367058
17
ENSE00001167890
chr1:
207649579-207649764
186
CR2_HUMAN
847-909
63
0
-
-
2.18
ENST00000367058
18
ENSE00001167878
chr1:
207651230-207651415
186
CR2_HUMAN
909-971
63
0
-
-
2.19
ENST00000367058
19
ENSE00001167866
chr1:
207652602-207652625
24
CR2_HUMAN
971-979
9
0
-
-
2.20
ENST00000367058
20
ENSE00001167855
chr1:
207653323-207653398
76
CR2_HUMAN
979-1004
26
0
-
-
2.21b
ENST00000367058
21b
ENSE00001246608
chr1:
207658809-207658917
109
CR2_HUMAN
1004-1033
30
0
-
-
2.22b
ENST00000367058
22b
ENSE00001841611
chr1:
207662487-207663240
754
CR2_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3oeda_ (A:)
1b: SCOP_d3oedb_ (B:)
2a: SCOP_d3oedc1 (C:0-65)
2b: SCOP_d3oedc2 (C:66-129)
2c: SCOP_d3oedd1 (D:0-65)
2d: SCOP_d3oedd2 (D:66-129)
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)
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)
Folds
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(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha/alpha toroid
(324)
Superfamily
:
Terpenoid cyclases/Protein prenyltransferases
(151)
Family
:
Complement components
(19)
Protein domain
:
Thio-ester containing domain (TED) from Complement C3, aka C3d or C3dg
(16)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d3oeda_
A:
1b
d3oedb_
B:
Class
:
Small proteins
(3458)
Fold
:
Complement control module/SCR domain
(70)
Superfamily
:
Complement control module/SCR domain
(70)
Family
:
Complement control module/SCR domain
(67)
Protein domain
:
automated matches
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d3oedc1
C:0-65
2b
d3oedc2
C:66-129
2c
d3oedd1
D:0-65
2d
d3oedd2
D:66-129
[
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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
(3, 8)
Info
all PFAM domains
1a: PFAM_A2M_comp_3oedB01 (B:58-291)
1b: PFAM_A2M_comp_3oedB02 (B:58-291)
2a: PFAM_Sushi_3oedD01 (D:71-126)
2b: PFAM_Sushi_3oedD02 (D:71-126)
2c: PFAM_Sushi_3oedD03 (D:71-126)
2d: PFAM_Sushi_3oedD04 (D:71-126)
3a: PFAM_Thiol_ester_cl_3oedB03 (B:6-36)
3b: PFAM_Thiol_ester_cl_3oedB04 (B:6-36)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
A2M_comp
(16)
Homo sapiens (Human)
(13)
1a
A2M_comp-3oedB01
B:58-291
1b
A2M_comp-3oedB02
B:58-291
Clan
:
no clan defined [family: Sushi]
(50)
Family
:
Sushi
(50)
Homo sapiens (Human)
(42)
2a
Sushi-3oedD01
D:71-126
2b
Sushi-3oedD02
D:71-126
2c
Sushi-3oedD03
D:71-126
2d
Sushi-3oedD04
D:71-126
Clan
:
no clan defined [family: Thiol-ester_cl]
(12)
Family
:
Thiol-ester_cl
(12)
Homo sapiens (Human)
(9)
3a
Thiol-ester_cl-3oedB03
B:6-36
3b
Thiol-ester_cl-3oedB04
B:6-36
[
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
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Chain C
Chain D
Asymmetric Unit 1
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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") .
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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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