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3EX7
Asym. Unit
Info
Asym.Unit (495 KB)
Biol.Unit 1 (243 KB)
Biol.Unit 2 (249 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF EJC IN ITS TRANSITION STATE
Authors
:
G. R. Andersen, K. H. Nielsen
Date
:
16 Oct 08 (Deposition) - 09 Dec 08 (Release) - 13 Jan 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,F (1x)
Biol. Unit 2: E,G,H,I,J (1x)
Keywords
:
Protein-Rna Complex, Mrna Processing, Mrna Splicing, Mrna Transport, Nonsense-Mediated Mrna Decay, Nucleus, Rna- Binding, Spliceosome, Transport, Alternative Splicing, Cytoplasm, Phosphoprotein, Acetylation, Atp-Binding, Helicase, Hydrolase, Nucleotide-Binding, Rrna Processing, Coiled Coil, Hydrolase/Rna Binding Protein/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. H. Nielsen, H. Chamieh, C. B. Andersen, F. Fredslund, K. Hamborg, H. Le Hir, G. R. Andersen
Mechanism Of Atp Turnover Inhibition In The Ejc
Rna V. 15 67 2009
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: ALUMINUM FLUORIDE (AF3a)
2b: ALUMINUM FLUORIDE (AF3b)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
AF3
2
Ligand/Ion
ALUMINUM FLUORIDE
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE C:40 , TYR C:56 , PHE C:58 , LYS C:60 , GLN C:65 , GLY C:85 , THR C:86 , GLY C:87 , LYS C:88 , THR C:89 , ALA C:90 , ASP C:342 , ARG C:370 , TYR C:371 , AF3 C:415 , MG C:416 , HOH C:421 , HOH C:497 , HOH C:508 , HOH C:569 , HOH C:572
BINDING SITE FOR RESIDUE ADP C 414
2
AC2
SOFTWARE
SER C:84 , GLY C:85 , LYS C:88 , GLU C:188 , ALA C:219 , GLY C:340 , ARG C:367 , ARG C:370 , ADP C:414 , MG C:416 , HOH C:417 , HOH C:461 , HOH C:569 , HOH C:570 , HOH C:571 , HOH C:572
BINDING SITE FOR RESIDUE AF3 C 415
3
AC3
SOFTWARE
THR C:89 , ADP C:414 , AF3 C:415 , HOH C:570 , HOH C:571 , HOH C:572
BINDING SITE FOR RESIDUE MG C 416
4
AC4
SOFTWARE
PHE H:40 , PHE H:58 , LYS H:60 , GLN H:65 , GLY H:85 , THR H:86 , GLY H:87 , LYS H:88 , THR H:89 , ALA H:90 , ASP H:342 , ARG H:370 , TYR H:371 , AF3 H:415 , MG H:416 , HOH H:456 , HOH H:489 , HOH H:492
BINDING SITE FOR RESIDUE ADP H 414
5
AC5
SOFTWARE
SER H:84 , GLY H:85 , LYS H:88 , GLU H:188 , ALA H:219 , GLY H:340 , ARG H:367 , ARG H:370 , ADP H:414 , MG H:416 , HOH H:419 , HOH H:421 , HOH H:489 , HOH H:490 , HOH H:491
BINDING SITE FOR RESIDUE AF3 H 415
6
AC6
SOFTWARE
THR H:89 , ASP H:187 , ADP H:414 , AF3 H:415 , HOH H:490 , HOH H:491 , HOH H:492
BINDING SITE FOR RESIDUE MG H 416
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_071090 (D270G, chain C/H, )
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)
---
C/H
D
270
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: Q_MOTIF (C:38-66,H:38-66)
2: RRM (B:73-151,G:73-151)
3: DEAD_ATP_HELICASE (C:185-193,H: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
C:38-66
H:38-66
2
RRM
PS50102
Eukaryotic RNA Recognition Motif (RRM) profile.
RBM8A_HUMAN
73-151
2
B:73-151
G:73-151
3
DEAD_ATP_HELICASE
PS00039
DEAD-box subfamily ATP-dependent helicases signature.
IF4A3_HUMAN
185-193
2
C:185-193
H:185-193
[
close PROSITE info
]
Exons
(19, 38)
Info
All Exons
Exon 1.5 (D:172-194 | I:167-194)
Exon 1.6 (D:216-249 | I:216-249)
Exon 2.1 (C:22-57 | H:22-57)
Exon 2.2 (C:57-81 | H:57-81)
Exon 2.3 (C:81-103 | H:81-103)
Exon 2.4 (C:104-124 | H:104-124)
Exon 2.5 (C:125-169 | H:125-169)
Exon 2.6 (C:169-196 | H:169-196)
Exon 2.7 (C:196-243 | H:196-243)
Exon 2.8 (C:243-289 | H:243-289)
Exon 2.9 (C:290-328 | H:290-328)
Exon 2.10 (C:328-364 | H:328-364)
Exon 2.11 (C:364-407 | H:364-407)
Exon 2.12 (C:407-411 | H:407-411)
Exon 3.1a (A:3-30 | E:5-30)
Exon 3.2 (A:30-49 | E:30-49)
Exon 3.3b (A:50-86 | E:50-86)
Exon 3.4 (A:87-114 | E:87-114)
Exon 3.5c (A:114-146 | E: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
D:172-194
I:167-194
23
28
1.6
ENST00000264645
6
ENSE00000863356
chr17:
38318978-38319154
177
CASC3_HUMAN
203-262
60
2
D:216-249
I:216-249
34
34
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
C:22-57
H:22-57
36
36
2.2
ENST00000269349
2
ENSE00000949585
chr17:
78118043-78117971
73
IF4A3_HUMAN
57-81
25
2
C:57-81
H:57-81
25
25
2.3
ENST00000269349
3
ENSE00000949586
chr17:
78115647-78115581
67
IF4A3_HUMAN
81-103
23
2
C:81-103
H:81-103
23
23
2.4
ENST00000269349
4
ENSE00000949587
chr17:
78115180-78115118
63
IF4A3_HUMAN
104-124
21
2
C:104-124
H:104-124
21
21
2.5
ENST00000269349
5
ENSE00001303885
chr17:
78113939-78113807
133
IF4A3_HUMAN
125-169
45
2
C:125-169
H:125-169
45
45
2.6
ENST00000269349
6
ENSE00000949589
chr17:
78113549-78113469
81
IF4A3_HUMAN
169-196
28
2
C:169-196
H:169-196
28
28
2.7
ENST00000269349
7
ENSE00000949591
chr17:
78112961-78112820
142
IF4A3_HUMAN
196-243
48
2
C:196-243
H:196-243
48
48
2.8
ENST00000269349
8
ENSE00001212947
chr17:
78112079-78111941
139
IF4A3_HUMAN
243-289
47
2
C:243-289
H:243-289
47
47
2.9
ENST00000269349
9
ENSE00001212937
chr17:
78111300-78111185
116
IF4A3_HUMAN
290-328
39
2
C:290-328
H:290-328
39
39
2.10
ENST00000269349
10
ENSE00000949595
chr17:
78110134-78110027
108
IF4A3_HUMAN
328-364
37
2
C:328-364
H:328-364
37
37
2.11
ENST00000269349
11
ENSE00001213013
chr17:
78109930-78109803
128
IF4A3_HUMAN
364-407
44
2
C:364-407
H:364-407
44
44
2.12
ENST00000269349
12
ENSE00001318045
chr17:
78109305-78109019
287
IF4A3_HUMAN
407-411
5
2
C:407-411
H:407-411
5
5
3.1a
ENST00000371470
1a
ENSE00001853117
chr1:
53704282-53704033
250
MGN_HUMAN
1-30
30
2
A:3-30
E:5-30
28
26
3.2
ENST00000371470
2
ENSE00001735272
chr1:
53701307-53701249
59
MGN_HUMAN
30-49
20
2
A:30-49
E:30-49
20
20
3.3b
ENST00000371470
3b
ENSE00001689792
chr1:
53699324-53699214
111
MGN_HUMAN
50-86
37
2
A:50-86
E:50-86
37
37
3.4
ENST00000371470
4
ENSE00001064642
chr1:
53694626-53694544
83
MGN_HUMAN
87-114
28
2
A:87-114
E:87-114
28
28
3.5c
ENST00000371470
5c
ENSE00001064645
chr1:
53692816-53692564
253
MGN_HUMAN
114-146
33
2
A:114-146
E:114-146
33
33
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ex7a_ (A:)
1b: SCOP_d3ex7e_ (E:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
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)
1a
d3ex7a_
A:
1b
d3ex7e_
E:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3ex7G00 (G:64-154)
1b: CATH_3ex7B00 (B:64-157)
2a: CATH_3ex7E00 (E:5-146)
2b: CATH_3ex7A00 (A:3-146)
View:
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Classes
(
)
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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
3ex7G00
G:64-154
1b
3ex7B00
B:64-157
Topology
:
Mago nashi protein
(10)
Homologous Superfamily
:
Mago nashi protein
(10)
Human (Homo sapiens)
(5)
2a
3ex7E00
E:5-146
2b
3ex7A00
A:3-146
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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