3ADL Gene Regulation Rna date Jan 22, 2010
title Structure Of Trbp2 And Its Molecule Implications For Mirna P
authors Y.A.Yuan, H.Y.Chen
compound source
Molecule: Risc-Loading Complex Subunit Tarbp2
Chain: A
Fragment: Drbm 2 Domain, Unp Residues 161-231
Synonym: Tar Rna-Binding Protein 2, Trans-Activation-Respon Binding Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tarbp2, Trbp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Rna (5'-R(Pcpgpcpgpcpgpcpgpcpg)-3')
Chain: B, C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Rna
symmetry Space Group: I 21 21 21
R_factor 0.261 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.300 60.425 99.892 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing., Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA, Structure. 2010 May 12;18(5):594-605. PMID:20462493
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (27 Kb) [Save to disk]
  • Biological Unit Coordinates (3adl.pdb1.gz) 22 Kb
  • CSU: Contacts of Structural Units for 3ADL
  • Structure Factors (128 Kb)
  • Retrieve 3ADL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ADL from S2C, [Save to disk]
  • Re-refined 3adl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ADL 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.
  • Visual 3D analysis of 3ADL
  • 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 3ADL, from MSDmotif at EBI
  • Fold representative 3adl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3adl_A] [3adl_B] [3adl_C] [3adl]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3ADL: [DSRM ] by SMART
  • Other resources with information on 3ADL
  • Community annotation for 3ADL 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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