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2XB2
Biol. Unit 2
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Asym.Unit (225 KB)
Biol.Unit 1 (110 KB)
Biol.Unit 2 (111 KB)
Biol.Unit 3 (5 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CORE MAGO-Y14-EIF4AIII-BARENTSZ-UPF3B ASSEMBLY SHOWS HOW THE EJC IS BRIDGED TO THE NMD MACHINERY
Authors
:
G. Buchwald, J. Ebert, C. Basquin, J. Sauliere, U. Jayachandran, F. Bono, H. Le Hir, E. Conti
Date
:
03 Apr 10 (Deposition) - 12 May 10 (Release) - 23 Jun 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A,C,D,E,F,G,R,S,T,U,X,Y,Z
Biol. Unit 1: R,S,U,X,Y,Z (1x)
Biol. Unit 2: A,C,D,E,G,T (1x)
Biol. Unit 3: F (1x)
Keywords
:
Exon Junction Complex, Nonsense-Mediated Mrna Decay, Translation, Upf3B, Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
G. Buchwald, J. Ebert, C. Basquin, J. Sauliere, U. Jayachandran, F. Bono, H. Le Hir, E. Conti
Insights Into The Recruitment Of The Nmd Machinery From The Crystal Structure Of A Core Ejc-Upf3B Complex.
Proc. Natl. Acad. Sci. Usa V. 107 10050 2010
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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: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:89 , ASP A:187 , GLU A:188 , ANP A:1413
BINDING SITE FOR RESIDUE MG A1412
2
AC2
SOFTWARE
PHE A:40 , PHE A:58 , LYS A:60 , PRO A:61 , GLN A:65 , SER A:84 , GLY A:85 , THR A:86 , 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
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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 A, )
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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)
---
A
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 (A:38-66)
2: RRM (D:73-151)
3: DEAD_ATP_HELICASE (A: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
A:38-66
-
2
RRM
PS50102
Eukaryotic RNA Recognition Motif (RRM) profile.
RBM8A_HUMAN
73-151
1
D:73-151
-
3
DEAD_ATP_HELICASE
PS00039
DEAD-box subfamily ATP-dependent helicases signature.
IF4A3_HUMAN
185-193
1
A:185-193
-
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2xb2D00 (D:66-154)
1b: CATH_2xb2Z00 (Z:66-154)
2a: CATH_2xb2C00 (C:4-146)
2b: CATH_2xb2Y00 (Y:4-146)
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Organisms
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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)
Human (Homo sapiens)
(81)
1a
2xb2D00
D:66-154
1b
2xb2Z00
Z:66-154
Topology
:
Mago nashi protein
(10)
Homologous Superfamily
:
Mago nashi protein
(10)
Human (Homo sapiens)
(5)
2a
2xb2C00
C:4-146
2b
2xb2Y00
Y:4-146
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Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_DEAD_2xb2X01 (X:62-228)
1b: PFAM_DEAD_2xb2X02 (X:62-228)
2a: PFAM_Helicase_C_2xb2X03 (X:295-372)
2b: PFAM_Helicase_C_2xb2X04 (X:295-372)
3a: PFAM_RRM_1_2xb2Z01 (Z:75-145)
3b: PFAM_RRM_1_2xb2Z02 (Z:75-145)
4a: PFAM_Btz_2xb2T01 (T:169-248)
4b: PFAM_Btz_2xb2T02 (T:169-248)
5a: PFAM_Mago_nashi_2xb2Y01 (Y:4-146)
5b: PFAM_Mago_nashi_2xb2Y02 (Y:4-146)
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Clans
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(
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Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
DEAD
(41)
Homo sapiens (Human)
(12)
1a
DEAD-2xb2X01
X:62-228
1b
DEAD-2xb2X02
X:62-228
Family
:
Helicase_C
(51)
Homo sapiens (Human)
(15)
2a
Helicase_C-2xb2X03
X:295-372
2b
Helicase_C-2xb2X04
X:295-372
Clan
:
RRM
(206)
Family
:
RRM_1
(131)
Homo sapiens (Human)
(94)
3a
RRM_1-2xb2Z01
Z:75-145
3b
RRM_1-2xb2Z02
Z:75-145
Clan
:
no clan defined [family: Btz]
(1)
Family
:
Btz
(1)
Homo sapiens (Human)
(1)
4a
Btz-2xb2T01
T:169-248
4b
Btz-2xb2T02
T:169-248
Clan
:
no clan defined [family: Mago_nashi]
(5)
Family
:
Mago_nashi
(5)
Homo sapiens (Human)
(2)
5a
Mago_nashi-2xb2Y01
Y:4-146
5b
Mago_nashi-2xb2Y02
Y:4-146
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Asymmetric Unit 1
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Asym.Unit (225 KB)
Header - Asym.Unit
Biol.Unit 1 (110 KB)
Header - Biol.Unit 1
Biol.Unit 2 (111 KB)
Header - Biol.Unit 2
Biol.Unit 3 (5 KB)
Header - Biol.Unit 3
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