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2J0Q
Asym. Unit
Info
Asym.Unit (235 KB)
Biol.Unit 1 (115 KB)
Biol.Unit 2 (115 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF THE EXON JUNCTION COMPLEX AT 3.2 A RESOLUTION
Authors
:
F. Bono, J. Ebert, E. Lorentzen, E. Conti
Date
:
04 Aug 06 (Deposition) - 30 Aug 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,T
Biol. Unit 1: A,C,D,E,T (1x)
Biol. Unit 2: B,F,G,H,I (1x)
Keywords
:
Hydrolase, Mrna Processing, Mrna Splicing, Mrna Transport, Nuclear Protein, Dead-Box Helicase, Rna-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Bono, J. Ebert, E. Lorentzen, E. Conti
The Crystal Structure Of The Exon Junction Complex Reveals How It Maintains A Stable Grip On Mrna.
Cell(Cambridge, Mass. ) V. 126 713 2006
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:89 , ASP A:187 , GLU A:188 , GLY A:340 , ANP A:1413
BINDING SITE FOR RESIDUE MG A1412
2
AC2
SOFTWARE
THR B:89 , ASP B:187 , GLU B:188 , ANP B:1413
BINDING SITE FOR RESIDUE MG B1412
3
AC3
SOFTWARE
PHE A:58 , LYS A:60 , GLN A:65 , SER A:84 , GLY A:85 , GLY A:87 , LYS A:88 , THR A:89 , ALA A:90 , GLU A:188 , GLY A:340 , ASP A:342 , ARG A:367 , ARG A:370 , TYR A:371 , MG A:1412
BINDING SITE FOR RESIDUE ANP A1413
4
AC4
SOFTWARE
PHE B:58 , LYS B:60 , GLN B:65 , SER B:84 , GLY B:85 , THR B:86 , GLY B:87 , LYS B:88 , THR B:89 , ALA B:90 , GLU B:188 , GLY B:340 , ASP B:342 , ARG B:367 , ARG B:370 , TYR B:371 , MG B:1412
BINDING SITE FOR RESIDUE ANP B1413
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_071090 (D270G, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_071090
D
270
G
IF4A3_HUMAN
Disease (RCPS)
---
A/B
D
270
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: Q_MOTIF (A:38-66,B:38-66)
2: RRM (D:73-151,G:73-151)
3: DEAD_ATP_HELICASE (A:185-193,B:185-193)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
Q_MOTIF
PS51195
DEAD-box RNA helicase Q motif profile.
IF4A3_HUMAN
38-66
2
A:38-66
B:38-66
2
RRM
PS50102
Eukaryotic RNA Recognition Motif (RRM) profile.
RBM8A_HUMAN
73-151
2
D:73-151
G:73-151
3
DEAD_ATP_HELICASE
PS00039
DEAD-box subfamily ATP-dependent helicases signature.
IF4A3_HUMAN
185-193
2
A:185-193
B:185-193
[
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]
Exons
(19, 38)
Info
All Exons
Exon 1.5 (I:168-196 | T:168-197)
Exon 1.6 (I:215-248 | T:214-248)
Exon 2.1 (A:22-57 | B:22-57)
Exon 2.2 (A:57-81 | B:57-81)
Exon 2.3 (A:81-103 | B:81-103)
Exon 2.4 (A:104-124 | B:104-124)
Exon 2.5 (A:125-169 | B:125-169)
Exon 2.6 (A:169-196 | B:169-196)
Exon 2.7 (A:196-243 | B:196-243)
Exon 2.8 (A:243-289 | B:243-289)
Exon 2.9 (A:290-328 | B:290-328)
Exon 2.10 (A:328-364 | B:328-364)
Exon 2.11 (A:364-407 | B:364-407)
Exon 2.12 (A:407-411 | B:407-411)
Exon 3.1a (C:4-30 | F:4-30)
Exon 3.2 (C:30-49 | F:30-49)
Exon 3.3b (C:50-86 | F:50-86)
Exon 3.4 (C:87-114 | F:87-114)
Exon 3.5c (C:114-146 | F:114-146)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.4a/1.5
02: Boundary 1.5/1.6
03: Boundary 1.6/1.7b
04: Boundary -/2.1
05: Boundary 2.1/2.2
06: Boundary 2.2/2.3
07: Boundary 2.3/2.4
08: Boundary 2.4/2.5
09: Boundary 2.5/2.6
10: Boundary 2.6/2.7
11: Boundary 2.7/2.8
12: Boundary 2.8/2.9
13: Boundary 2.9/2.10
14: Boundary 2.10/2.11
15: Boundary 2.11/2.12
16: Boundary 2.12/-
17: Boundary -/3.1a
18: Boundary 3.1a/3.2
19: Boundary 3.2/3.3b
20: Boundary 3.3b/3.4
21: Boundary 3.4/3.5c
22: Boundary 3.5c/-
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
ENST00000264645
1a
ENSE00001517546
chr17:
38296507-38297032
526
CASC3_HUMAN
1-77
77
0
-
-
1.2
ENST00000264645
2
ENSE00000720185
chr17:
38297460-38297487
28
CASC3_HUMAN
78-87
10
0
-
-
1.3
ENST00000264645
3
ENSE00001120433
chr17:
38297823-38297860
38
CASC3_HUMAN
87-99
13
0
-
-
1.4a
ENST00000264645
4a
ENSE00000863354
chr17:
38318006-38318164
159
CASC3_HUMAN
100-152
53
0
-
-
1.5
ENST00000264645
5
ENSE00000863355
chr17:
38318255-38318406
152
CASC3_HUMAN
153-203
51
2
I:168-196
T:168-197
29
30
1.6
ENST00000264645
6
ENSE00000863356
chr17:
38318978-38319154
177
CASC3_HUMAN
203-262
60
2
I:215-248
T:214-248
34
35
1.7b
ENST00000264645
7b
ENSE00000863357
chr17:
38319734-38320419
686
CASC3_HUMAN
262-491
230
0
-
-
1.8b
ENST00000264645
8b
ENSE00000863358
chr17:
38323050-38323114
65
CASC3_HUMAN
491-512
22
0
-
-
1.9
ENST00000264645
9
ENSE00000900529
chr17:
38323751-38323865
115
CASC3_HUMAN
513-551
39
0
-
-
1.10
ENST00000264645
10
ENSE00000950687
chr17:
38324103-38324201
99
CASC3_HUMAN
551-584
34
0
-
-
1.11b
ENST00000264645
11b
ENSE00000900527
chr17:
38324456-38324670
215
CASC3_HUMAN
584-655
72
0
-
-
1.12
ENST00000264645
12
ENSE00001322421
chr17:
38325577-38325699
123
CASC3_HUMAN
656-696
41
0
-
-
1.13a
ENST00000264645
13a
ENSE00001350371
chr17:
38325851-38325915
65
CASC3_HUMAN
697-703
7
0
-
-
1.13c
ENST00000264645
13c
ENSE00001350362
chr17:
38326700-38328431
1732
CASC3_HUMAN
-
0
0
-
-
2.1
ENST00000269349
1
ENSE00001213025
chr17:
78120938-78120592
347
IF4A3_HUMAN
1-57
57
2
A:22-57
B:22-57
36
36
2.2
ENST00000269349
2
ENSE00000949585
chr17:
78118043-78117971
73
IF4A3_HUMAN
57-81
25
2
A:57-81
B:57-81
25
25
2.3
ENST00000269349
3
ENSE00000949586
chr17:
78115647-78115581
67
IF4A3_HUMAN
81-103
23
2
A:81-103
B:81-103
23
23
2.4
ENST00000269349
4
ENSE00000949587
chr17:
78115180-78115118
63
IF4A3_HUMAN
104-124
21
2
A:104-124
B:104-124
21
21
2.5
ENST00000269349
5
ENSE00001303885
chr17:
78113939-78113807
133
IF4A3_HUMAN
125-169
45
2
A:125-169
B:125-169
45
45
2.6
ENST00000269349
6
ENSE00000949589
chr17:
78113549-78113469
81
IF4A3_HUMAN
169-196
28
2
A:169-196
B:169-196
28
28
2.7
ENST00000269349
7
ENSE00000949591
chr17:
78112961-78112820
142
IF4A3_HUMAN
196-243
48
2
A:196-243
B:196-243
48
48
2.8
ENST00000269349
8
ENSE00001212947
chr17:
78112079-78111941
139
IF4A3_HUMAN
243-289
47
2
A:243-289
B:243-289
47
47
2.9
ENST00000269349
9
ENSE00001212937
chr17:
78111300-78111185
116
IF4A3_HUMAN
290-328
39
2
A:290-328
B:290-328
39
39
2.10
ENST00000269349
10
ENSE00000949595
chr17:
78110134-78110027
108
IF4A3_HUMAN
328-364
37
2
A:328-364
B:328-364
37
37
2.11
ENST00000269349
11
ENSE00001213013
chr17:
78109930-78109803
128
IF4A3_HUMAN
364-407
44
2
A:364-407
B:364-407
44
44
2.12
ENST00000269349
12
ENSE00001318045
chr17:
78109305-78109019
287
IF4A3_HUMAN
407-411
5
2
A:407-411
B:407-411
5
5
3.1a
ENST00000371470
1a
ENSE00001853117
chr1:
53704282-53704033
250
MGN_HUMAN
1-30
30
2
C:4-30
F:4-30
27
27
3.2
ENST00000371470
2
ENSE00001735272
chr1:
53701307-53701249
59
MGN_HUMAN
30-49
20
2
C:30-49
F:30-49
20
20
3.3b
ENST00000371470
3b
ENSE00001689792
chr1:
53699324-53699214
111
MGN_HUMAN
50-86
37
2
C:50-86
F:50-86
37
37
3.4
ENST00000371470
4
ENSE00001064642
chr1:
53694626-53694544
83
MGN_HUMAN
87-114
28
2
C:87-114
F:87-114
28
28
3.5c
ENST00000371470
5c
ENSE00001064645
chr1:
53692816-53692564
253
MGN_HUMAN
114-146
33
2
C:114-146
F:114-146
33
33
[
close EXON info
]
SCOP Domains
(3, 8)
Info
All SCOP Domains
1a: SCOP_d2j0qd1 (D:66-154)
1b: SCOP_d2j0qg1 (G:66-154)
2a: SCOP_d2j0qc1 (C:4-145)
2b: SCOP_d2j0qf1 (F:4-145)
3a: SCOP_d2j0qa1 (A:22-243)
3b: SCOP_d2j0qa2 (A:244-411)
3c: SCOP_d2j0qb1 (B:22-243)
3d: SCOP_d2j0qb2 (B:244-411)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
RNA-binding domain, RBD
(289)
Family
:
Canonical RBD
(214)
Protein domain
:
RNA-binding protein 8
(6)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d2j0qd1
D:66-154
1b
d2j0qg1
G:66-154
Fold
:
Mago nashi protein
(8)
Superfamily
:
Mago nashi protein
(8)
Family
:
Mago nashi protein
(8)
Protein domain
:
Mago nashi protein
(8)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d2j0qc1
C:4-145
2b
d2j0qf1
F:4-145
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Tandem AAA-ATPase domain
(59)
Protein domain
:
Probable ATP-dependent RNA helicase DDX48
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
3a
d2j0qa1
A:22-243
3b
d2j0qa2
A:244-411
3c
d2j0qb1
B:22-243
3d
d2j0qb2
B:244-411
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2j0qD00 (D:66-154)
1b: CATH_2j0qG00 (G:66-154)
2a: CATH_2j0qC00 (C:4-146)
2b: CATH_2j0qF00 (F:4-146)
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Organisms
(
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(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.330, no name defined]
(307)
Human (Homo sapiens)
(81)
1a
2j0qD00
D:66-154
1b
2j0qG00
G:66-154
Topology
:
Mago nashi protein
(10)
Homologous Superfamily
:
Mago nashi protein
(10)
Human (Homo sapiens)
(5)
2a
2j0qC00
C:4-146
2b
2j0qF00
F:4-146
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
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Asym.Unit (235 KB)
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