OCA Atlas for 2XB2

2XB2

Hydrolase

date

Apr 03, 2010

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

compound

source

Molecule: Eukaryotic Initiation Factor 4a-III
Chain: A, X
Synonym: Eif4aiii, Eukaryotic Translation Initiation Factor 4a Isoform 3, Atp-Dependent Rna Helicase Eif4a-3, Atp-Dependent Rna Helicase Ddx48, Dead Box Protein 48, Eukaryotic Initiation Factor 4a-Like Nuk-34, Nuclear Matrix Protein 265, Nmp 265;
Ec: 3.6.1.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Petmcn

Molecule: Rna Poly-U-Ribonucleotide
Chain: E, R
Other_details: 15 Poly-U Synthetic Construct

Synthetic: Yes

Molecule: Regulator Of Nonsense Transcripts 3b
Chain: G, U
Fragment: C-Terminal Ejc Binding Region, Residues 411-470
Synonym: Upf3b, Nonsense Mrna Reducing Factor 3b, Up-Frameshift Suppressor 3 Homolog B, Up-Frameshift Suppressor 3 Homolog On Chromosome X, Hupf3p-X;
Engineered: Yes

Molecule: Putative Regulator Of Nonsense Transcripts 3b
Chain: F

Molecule: Rna-Binding Protein 8a
Chain: D, Z
Fragment: Rrm, Residues 66-155
Synonym: Rna-Binding Motif Protein 8a, Y14, Ribonucleoprotein Rbm8a, Rna-Binding Protein Y14, Binder Of Ovca1-1, Bov-1;
Engineered: Yes

Molecule: Protein Mago Nashi Homolog
Chain: C, Y
Synonym: Mago
Engineered: Yes

Molecule: Protein Casc3
Chain: T, S
Fragment: Selor Domain, Residues 137-286
Synonym: Barentsz, Cancer Susceptibility Candidate Gene 3 Protein, Metastatic Lymph Node Gene 51 Protein, Mln 51, Btz;
Engineered: Yes

symmetry

Space Group: P 41 21 2

R_factor

0.2204

R_Free

0.2604

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
134.800	134.800	227.250	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.40 Å

ligand

ANP, MG

enzyme

Hydrolase E.C.3.6.1 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, X	nucleotide binding nucleic acid binding RNA binding ATP-dependent RNA helicase a... helicase activity protein binding ATP binding ATP-dependent helicase activ... poly(A) RNA binding hydrolase activity	nuclear-transcribed mRNA cat... nuclear-transcribed mRNA cat... nuclear-transcribed mRNA pol... mRNA splicing, via spliceoso... rRNA processing mRNA processing regulation of translation transport RNA splicing gene expression RNA metabolic process mRNA metabolic process negative regulation of trans... cytokine-mediated signaling ... positive regulation of trans... mRNA transport	nucleus spliceosomal complex cytoplasm cytosol nuclear speck exon-exon junction complex catalytic step 2 spliceosome...
C, Y	RNA binding protein binding	nuclear-transcribed mRNA cat... mRNA splicing, via spliceoso... transcription from RNA polym... termination of RNA polymeras... mRNA processing mRNA export from nucleus regulation of translation transport RNA splicing gene expression RNA metabolic process mRNA metabolic process mRNA 3'-end processing mRNA transport	nucleus nucleoplasm spliceosomal complex cytoplasm cytosol nuclear speck exon-exon junction complex catalytic step 2 spliceosome...

Primary reference

Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex., Buchwald G, Ebert J, Basquin C, Sauliere J, Jayachandran U, Bono F, Le Hir H, Conti E, Proc Natl Acad Sci U S A. 2010 May 17. PMID:20479275

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (224 Kb) [Save to disk]

Biological Unit Coordinates (2xb2.pdb1.gz) 110 Kb

Biological Unit Coordinates (2xb2.pdb2.gz) 110 Kb

Biological Unit Coordinates (2xb2.pdb3.gz) 5 Kb

LPC: Ligand-Protein Contacts for 2XB2

CSU: Contacts of Structural Units for 2XB2

Structure Factors (246 Kb)

Retrieve 2XB2 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2XB2 from S2C, [Save to disk]

Re-refined 2xb2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2XB2 in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

On AstexViewer, from MSD-EBI (viewer documentation).

On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2XB2

Cartoon representation from PDB Cartoon

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

Crystal Contacts, from CryCo at Weizmann Institute

3D motif for 2XB2, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1q2xb2, region B:134-357 [Jmol] [rasmolscript] [script source]
- Domain d1w2xb2, region B:1815-2189 [Jmol] [rasmolscript] [script source]
- Domain d1n2xb2, region B:8-114,B:216-292 [Jmol] [rasmolscript] [script source]

Fold representative 2xb2 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2xb2_A] [2xb2_C] [2xb2_D] [2xb2_E] [2xb2_F] [2xb2_G] [2xb2_R] [2xb2_S] [2xb2_T] [2xb2_U] [2xb2_X] [2xb2_Y] [2xb2_Z]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Alignments of the sequence of 2XB2 with the sequences similar proteins can be viewed for 2XB2's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.

A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 2XB2

Community annotation for 2XB2 at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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