OCA Atlas for 2J0Q

2J0Q

Hydrolase

date

Aug 04, 2006

title

The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution

authors

F.Bono, J.Ebert, E.Lorentzen, E.Conti

compound

source

Molecule: Atp-Dependent Rna Helicase Ddx48
Chain: A, B
Synonym: Eif4aiii Rna-Helicase, Dead Box Protein 48, Eukary Initiation Factor 4a-Like Nuk-34, Hnmp 265, Nuclear Matrix 265, Eukaryotic Translation Initiation Factor 4a Isoform 3
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_type: Plasmid
Expression_system_vector: Petmcn

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

Molecule: Rna-Binding Protein 8a
Chain: D, G
Fragment: Residues 66-174
Synonym: Y14, Rna-Binding Motif Protein 8a, Ribonucleoprote Rbm8a, Rna-Binding Protein Y14, Binder Of Ovca1-1, Bov-1;
Engineered: Yes

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

Molecule: 5'-R(Upupupupupupupupupupupupupupu
Chain: E, H

Synthetic: Yes

symmetry

Space Group: P 21 21 21

R_factor

0.232

R_Free

0.277

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
69.150	161.240	193.240	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.20 Å

ligand

ANP, MG

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, B	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...
F, C	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

The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA., Bono F, Ebert J, Lorentzen E, Conti E, Cell. 2006 Aug 25;126(4):713-25. PMID:16923391

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (235 Kb) [Save to disk]

Biological Unit Coordinates (2j0q.pdb1.gz) 114 Kb

Biological Unit Coordinates (2j0q.pdb2.gz) 114 Kb

LPC: Ligand-Protein Contacts for 2J0Q

CSU: Contacts of Structural Units for 2J0Q

Likely Quarternary Molecular Structure file(s) for 2J0Q

Structure Factors (497 Kb)

Retrieve 2J0Q in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2J0Q from S2C, [Save to disk]

Re-refined 2j0q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2J0Q 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 2J0Q

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 2J0Q, from MSDmotif at EBI

Fold representative 2j0q from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2j0q_A] [2j0q_B] [2j0q_C] [2j0q_D] [2j0q_F] [2j0q_G] [2j0q_I] [2j0q_T] [2j0q_E] [2j0q_H]

SWISS-PROT database: [O15234] [P38919] [P61326] [Q9Y5S9]

Belongs to the nuclear mrna exporter (mrna-e) family

according to TCDB.

Domain organization of [CASC3_HUMAN] [IF4A3_HUMAN] [MGN_HUMAN] [RBM8A_HUMAN] by SWISSPFAM

Domains found in 2J0Q: [Btz] [DEXDc] [HELICc] [RRM ] by SMART

Alignments of the sequence of 2J0Q with the sequences similar proteins can be viewed for 2J0Q's classification [CASC3_HUMAN] [IF4A3_HUMAN] [MGN_HUMAN] [RBM8A_HUMAN] 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 [CASC3_HUMAN] [IF4A3_HUMAN] [MGN_HUMAN] [RBM8A_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2J0Q

Community annotation for 2J0Q at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]