3PUF

Crystal structure of human RNase H2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutieres syndrome defects.

Figiel, M.Chon, H.Cerritelli, S.M.Cybulska, M.Crouch, R.J.Nowotny, M.

(2011) J Biol Chem 286: 10540-10550

  • DOI: 10.1074/jbc.M110.181974
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutières syndrome, a severe autoim ...

    RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutières syndrome, a severe autoimmune disorder. The 3.1 Å crystal structure of human RNase H2 presented here allowed us to map the positions of all 29 mutations found in Aicardi-Goutières syndrome patients, several of which were not visible in the previously reported mouse RNase H2. We propose the possible effects of these mutations on the protein stability and function. Bacterial and eukaryotic RNases H2 differ in composition and substrate specificity. Bacterial RNases H2 are monomeric proteins and homologs of the eukaryotic RNases H2 catalytic subunit, which in addition possesses two accessory proteins. The eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and (5')RNA-DNA(3')/DNA junction hybrids as substrates with similar efficiency, whereas bacterial RNases H2 are highly specialized in the recognition of the (5')RNA-DNA(3') junction and very poorly cleave RNA/DNA hybrids in the presence of Mg(2+) ions. Using the crystal structure of the Thermotoga maritima RNase H2-substrate complex, we modeled the human RNase H2-substrate complex and verified the model by mutational analysis. Our model indicates that the difference in substrate preference stems from the different position of the crucial tyrosine residue involved in substrate binding and recognition.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw 02-109, Poland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H2 subunit AA, D, G, J, M, P302Homo sapiensMutation(s): 0 
Gene Names: RNASEH2ARNASEHIRNHIA
EC: 3.1.26.4
Find proteins for O75792 (Homo sapiens)
Explore O75792 
Go to UniProtKB:  O75792
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PHAROS  O75792
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H2 subunit BB, E, H, K, N, Q224Homo sapiensMutation(s): 0 
Gene Names: RNASEH2BDLEU8
EC: 3.1.26.4
Find proteins for Q5TBB1 (Homo sapiens)
Explore Q5TBB1 
Go to UniProtKB:  Q5TBB1
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PHAROS  Q5TBB1
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H2 subunit CC, F, I, L, O, R167Homo sapiensMutation(s): 0 
Gene Names: RNASEH2CAYP1
EC: 3.1.26.4
Find proteins for Q8TDP1 (Homo sapiens)
Explore Q8TDP1 
Go to UniProtKB:  Q8TDP1
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PHAROS  Q8TDP1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.068α = 105.9
b = 108.366β = 103.71
c = 114.264γ = 111.42
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-08-29
    Changes: Database references