Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.208 

Starting Model: experimental
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Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription

Nowotny, M.Gaidamakov, S.A.Ghirlando, R.Cerritelli, S.M.Crouch, R.J.Yang, W.

(2007) Mol Cell 28: 264-276

  • DOI: https://doi.org/10.1016/j.molcel.2007.08.015
  • Primary Citation of Related Structures:  
    2QK9, 2QKB, 2QKK

  • PubMed Abstract: 

    We report here crystal structures of human RNase H1 complexed with an RNA/DNA substrate. Unlike B. halodurans RNase H1, human RNase H1 has a basic protrusion, which forms a DNA-binding channel and together with the conserved phosphate-binding pocket confers specificity for the B form and 2'-deoxy DNA. The RNA strand is recognized by four consecutive 2'-OH groups and cleaved by a two-metal ion mechanism. Although RNase H1 is overall positively charged, the substrate interface is neutral to acidic in character, which likely contributes to the catalytic specificity. Positions of the scissile phosphate and two catalytic metal ions are interdependent and highly coupled. Modeling of HIV reverse transcriptase (RT) with RNA/DNA in its RNase H active site suggests that the substrate cannot simultaneously occupy the polymerase active site and must undergo a conformational change to toggle between the two catalytic centers. The region that accommodates this conformational change offers a target to develop HIV-specific inhibitors.

  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease H1C [auth A],
D [auth B]
154Homo sapiensMutation(s): 1 
Gene Names: RNASEH1RNH1
UniProt & NIH Common Fund Data Resources
Find proteins for O60930 (Homo sapiens)
Explore O60930 
Go to UniProtKB:  O60930
PHAROS:  O60930
GTEx:  ENSG00000171865 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60930
Sequence Annotations
  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.991α = 90
b = 109.991β = 90
c = 67.253γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-07-28
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection