3D9K Transcription date May 27, 2008
title Snapshots Of The Rna Processing Factor Scaf8 Bound To Differ Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna- II
authors R.Becker, B.Loll, A.Meinhart
compound source
Molecule: Rna-Binding Protein 16
Chain: A, B
Fragment: Ctd Interacting Domain Of Scaf8, Unp Residues 1-1
Synonym: Rna-Binding Motif Protein 16
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Man
Organism_taxid: 9606
Gene: Rbm16, Kiaa1116
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ctd-Peptide
Chain: Y, Z
Engineered: Yes

Synthetic: Yes
Other_details: Peptide Derived From The Conserved Repeat Se Rna Polymerase II Ctd
symmetry Space Group: P 43
R_factor 0.190 R_Free 0.252
length a length b length c angle alpha angle beta angle gamma
56.450 56.450 106.270 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand SEP, SO4 enzyme
Primary referenceSnapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxy-terminal domain of RNA-polymerase II., Becker R, Loll B, Meinhart A, J Biol Chem. 2008 Jun 11. PMID:18550522
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (3d9k.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (3d9k.pdb2.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 3D9K
  • CSU: Contacts of Structural Units for 3D9K
  • Likely Quarternary Molecular Structure file(s) for 3D9K
  • Structure Factors (126 Kb)
  • Retrieve 3D9K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D9K from S2C, [Save to disk]
  • Re-refined 3d9k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D9K 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 3D9K
  • 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 3D9K, from MSDmotif at EBI
  • Fold representative 3d9k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d9k_Z] [3d9k] [3d9k_Y] [3d9k_A] [3d9k_B]
  • SWISS-PROT database: [Q9UPN6]
  • Domain organization of [RBM16_HUMAN] by SWISSPFAM
  • Domain found in 3D9K: [RPR ] by SMART
  • Other resources with information on 3D9K
  • Community annotation for 3D9K 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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