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2HYI
Biol. Unit 1
Info
Asym.Unit (250 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (123 KB)
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(1)
Title
:
STRUCTURE OF THE HUMAN EXON JUNCTION COMPLEX WITH A TRAPPED DEAD-BOX HELICASE BOUND TO RNA
Authors
:
C. B. F. Andersen, H. Le Hir, G. R. Andersen
Date
:
06 Aug 06 (Deposition) - 15 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,F,G,H,I,J,L
Biol. Unit 1: A,B,C,D,F (1x)
Biol. Unit 2: G,H,I,J,L (1x)
Keywords
:
Exon Junction, Splicing, Mrna Processing, Translation, Dead- Box Atpase, Nonsense Mediated Decay, Hydrolase/Rna Binding Protein/Rna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
C. B. F. Andersen, L. Ballut, J. S. Johansen, H. Chamieh, K. H. Nielsen, C. L. Oliveira, J. S. Pedersen, B. Seraphin, H. Le Hir, G. R. Andersen
Structure Of The Exon Junction Core Complex With A Trapped Dead-Box Atpase Bound To Rna.
Science V. 313 1968 2006
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
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No.
Name
Count
Type
Full Name
1
ANP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR C:89 , ASP C:187 , ANP C:801 , HOH C:802 , HOH C:803 , HOH C:804
BINDING SITE FOR RESIDUE MG C 701
2
AC3
SOFTWARE
PHE C:58 , LYS C:60 , GLN C:65 , SER C:84 , GLY C:85 , THR C:86 , GLY C:87 , LYS C:88 , THR C:89 , ALA C:90 , GLU C:188 , GLY C:340 , ASP C:342 , ARG C:367 , ARG C:370 , TYR C:371 , MG C:701 , HOH C:803 , HOH C:805 , HOH C:810 , HOH C:812 , HOH C:837 , HOH C:859 , HOH C:866 , HOH C:887 , HOH C:947
BINDING SITE FOR RESIDUE ANP C 801
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_071090 (D270G, chain C, )
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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
D
270
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: Q_MOTIF (C:38-66)
2: RRM (B:73-151)
3: DEAD_ATP_HELICASE (C:185-193)
;
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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
1
C:38-66
-
2
RRM
PS50102
Eukaryotic RNA Recognition Motif (RRM) profile.
RBM8A_HUMAN
73-151
1
B:73-151
-
3
DEAD_ATP_HELICASE
PS00039
DEAD-box subfamily ATP-dependent helicases signature.
IF4A3_HUMAN
185-193
1
C:185-193
-
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 8)
Info
All SCOP Domains
1a: SCOP_d2hyib_ (B:)
1b: SCOP_d2hyih_ (H:)
2a: SCOP_d2hyia_ (A:)
2b: SCOP_d2hyig_ (G:)
3a: SCOP_d2hyic1 (C:22-243)
3b: SCOP_d2hyic2 (C:244-411)
3c: SCOP_d2hyii1 (I:22-243)
3d: SCOP_d2hyii2 (I:244-413)
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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
d2hyib_
B:
1b
d2hyih_
H:
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
d2hyia_
A:
2b
d2hyig_
G:
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
d2hyic1
C:22-243
3b
d2hyic2
C:244-411
3c
d2hyii1
I:22-243
3d
d2hyii2
I:244-413
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2hyiB00 (B:64-154)
1b: CATH_2hyiH00 (H:64-154)
2a: CATH_2hyiA00 (A:3-146)
2b: CATH_2hyiG00 (G:3-146)
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)
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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)
[unclassified]
(45)
1a
2hyiB00
B:64-154
1b
2hyiH00
H:64-154
Topology
:
Mago nashi protein
(10)
Homologous Superfamily
:
Mago nashi protein
(10)
[unclassified]
(1)
2a
2hyiA00
A:3-146
2b
2hyiG00
G:3-146
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (250 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (123 KB)
Header - Biol.Unit 2
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