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- PDB-3p5j: The structure of the human RNase H2 complex defines key interacti... -

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Basic information

Entry
Database: PDB / ID: 3p5j
TitleThe structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease
Components
  • Ribonuclease H2 subunit A
  • Ribonuclease H2 subunit B
  • Ribonuclease H2 subunit C
KeywordsHYDROLASE/REPLICATION / RNase H2 fold / triple beta-barrel / Nuclease that cleaves RNA/DNA hybrids / Proliferating Cell Nuclear Antigen (PCNA) and RNA/DNA hybrids / nucleus / HYDROLASE-REPLICATION complex
Function / homology
Function and homology information


ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity ...ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / RNA-DNA hybrid ribonuclease activity / gene expression / fibroblast proliferation / in utero embryonic development / negative regulation of gene expression / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Histone, subunit A - #120 / N-terminal domain of TfIIb - #530 / Lipocalin - #680 / Ribonuclease H2, subunit C / Ribonuclease H2 non-catalytic subunit (Ylr154p-like) / Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain ...Histone, subunit A - #120 / N-terminal domain of TfIIb - #530 / Lipocalin - #680 / Ribonuclease H2, subunit C / Ribonuclease H2 non-catalytic subunit (Ylr154p-like) / Ribonuclease H2 subunit B, wHTH domain / Ribonuclease H2 subunit B / Rnh202, triple barrel domain / Ydr279p protein family (RNase H2 complex component) wHTH domain / Ydr279p protein triple barrel domain / Ribonuclease hii. Domain 2 / Ribonuclease H2, subunit A / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease (RNase) H type-2 domain profile. / Ribonuclease HII/HIII / Ribonuclease HII/HIII domain / Ribonuclease HII / Histone, subunit A / N-terminal domain of TfIIb / Single Sheet / Ribonuclease H-like superfamily/Ribonuclease H / Lipocalin / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribonuclease H2 subunit B / Ribonuclease H2 subunit C / Ribonuclease H2 subunit A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.9 Å
AuthorsBubeck, D. / Graham, S.C. / Jones, E.Y.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction.
Authors: Shaban, N.M. / Harvey, S. / Perrino, F.W. / Hollis, T.
History
DepositionOct 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 0THIS ENTRY 3P5J REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3KIOSF DETERMINED ...THIS ENTRY 3P5J REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3KIOSF DETERMINED BY AUTHORS OF THE PDB ENTRY 3KIO: N.Shaban,D.Harvey,F.W.Perrino,T.Hollis.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H2 subunit A
B: Ribonuclease H2 subunit B
C: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)88,8903
Polymers88,8903
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-62 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.290, 40.420, 67.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonuclease H2 subunit A / RNase H2 subunit A / Ribonuclease HI large subunit / RNase HI large subunit / Ribonuclease HI subunit A


Mass: 33547.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnaseh2a, Rnasehi / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CWY8, ribonuclease H
#2: Protein Ribonuclease H2 subunit B / RNase H2 subunit B / Deleted in lymphocytic leukemia 8 homolog / Ribonuclease HI subunit B


Mass: 37494.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnaseh2b, Dleu8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80ZV0
#3: Protein Ribonuclease H2 subunit C / RNase H2 subunit C / Ribonuclease HI subunit C


Mass: 17848.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnaseh2c, Ayp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQ18

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.88 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3KIO.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 62.11 Å2

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→24.61 Å / Cor.coef. Fo:Fc: 0.8969 / Cor.coef. Fo:Fc free: 0.8348 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: This is a re-refinement of the murine RNase H2 coordinates previously deposited by Shaban et al., 2010 (PDB ID 3KIO)
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 925 5.2 %RANDOM
Rwork0.21 ---
obs0.2132 17777 --
Displacement parametersBiso mean: 62.48 Å2
Baniso -1Baniso -2Baniso -3
1-13.0671 Å20 Å20 Å2
2---4.4747 Å20 Å2
3----8.5923 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: LAST / Resolution: 2.9→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 0 0 4016
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114116HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.285614HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1269SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes630HARMONIC5
X-RAY DIFFRACTIONt_it4116HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion21.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5485
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact46444
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2934 163 5.8 %
Rwork0.229 2649 -
all0.2326 2812 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1145-0.29480.71021.2523-0.52222.3424-0.0432-0.0372-0.12810.01490.0176-0.0206-0.06510.12220.02570.1858-0.0251-0.0022-0.2376-0.0287-0.30473.20079.682422.1632
25.93262.5634-0.11130.0013-0.38880.4014-0.0230.1306-0.1646-0.13360.02690.54420.0586-0.3411-0.004-0.304-0.0503-0.042-0.2907-0.08410.30422.3709-7.18933.4824
34.55190.21110.93063.62130.86951.56010.10050.2979-0.4617-0.1266-0.09830.54420.197-0.1822-0.00210.0704-0.0255-0.0155-0.2576-0.0167-0.168345.4622-2.77824.2073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 299
2X-RAY DIFFRACTION2{ B|* }B11 - 231
3X-RAY DIFFRACTION3{ C|* }C14 - 162

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