3BSU Hydrolase Rna Dna date Dec 26, 2007
title Hybrid-Binding Domain Of Human Rnase H1 In Complex With 12- Mer Rnadna
authors M.Nowotny, S.M.Cerritelli, R.Ghirlando, S.A.Gaidamakov, R.J.Crouch, W.Yang
compound source
Molecule: Ribonuclease H1
Chain: A, B, C, F, G, H
Fragment: Catalytic Domain
Synonym: Rnase H1; Ribonuclease H Type II
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnaseh1, Rnh1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15

Molecule: Rna (5'-R(Gpapcpapcpcpupgpapupupc)- 3');
Chain: D, I
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Dgpdapdapdtpdcpdapdgpdgp(5iu) Pdgpdtpdc)-3');
Chain: E, J
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.220 R_Free 0.290
length a length b length c angle alpha angle beta angle gamma
45.492 64.262 140.322 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 5IU, MG enzyme Hydrolase E.C. BRENDA
note 3BSU is a representative structure
Primary referenceSpecific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD., Nowotny M, Cerritelli SM, Ghirlando R, Gaidamakov SA, Crouch RJ, Yang W, EMBO J. 2008 Mar 13;. PMID:18337749
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (3bsu.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (3bsu.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 3BSU
  • CSU: Contacts of Structural Units for 3BSU
  • Likely Quarternary Molecular Structure file(s) for 3BSU
  • Structure Factors (214 Kb)
  • Retrieve 3BSU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BSU from S2C, [Save to disk]
  • Re-refined 3bsu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BSU 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 3BSU
  • 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 3BSU, from MSDmotif at EBI
  • Fold representative 3bsu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bsu_G] [3bsu_C] [3bsu_I] [3bsu_H] [3bsu] [3bsu_E] [3bsu_D] [3bsu_B] [3bsu_A] [3bsu_F] [3bsu_J]
  • SWISS-PROT database: [O60930]
  • Domain organization of [RNH1_HUMAN] by SWISSPFAM
  • Other resources with information on 3BSU
  • Community annotation for 3BSU 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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