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- PDB-3p56: The structure of the human RNase H2 complex defines key interacti... -

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Basic information

Entry
Database: PDB / ID: 3p56
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 H 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 / RNA nuclease activity / mismatch repair / regulation of G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation ...ribonucleotide metabolic process / ribonuclease H2 complex / DNA replication, removal of RNA primer / regulation of DNA damage checkpoint / RNA catabolic process / ribonuclease H / RNA nuclease activity / 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 / DNA replication / in utero embryonic development / negative regulation of gene expression / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
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 H2, subunit A / Ribonuclease HII, helix-loop-helix cap domain superfamily / Ribonuclease (RNase) H type-2 domain profile. ...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 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Ribonuclease H2 subunit A / Ribonuclease H2 subunit B / Ribonuclease H2 subunit C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.06 Å
AuthorsBubeck, D. / Graham, S.C. / Jones, E.Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Structure of the Human RNase H2 Complex Defines Key Interaction Interfaces Relevant to Enzyme Function and Human Disease.
Authors: Reijns, M.A. / Bubeck, D. / Gibson, L.C. / Graham, S.C. / Baillie, G.S. / Jones, E.Y. / Jackson, A.P.
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 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
D: Ribonuclease H2 subunit A
E: Ribonuclease H2 subunit B
F: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)155,8116
Polymers155,8116
Non-polymers00
Water00
1
A: Ribonuclease H2 subunit A
B: Ribonuclease H2 subunit B
C: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)77,9063
Polymers77,9063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-54 kcal/mol
Surface area25340 Å2
MethodPISA
2
D: Ribonuclease H2 subunit A
E: Ribonuclease H2 subunit B
F: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)77,9063
Polymers77,9063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-56 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.238, 42.302, 186.950
Angle α, β, γ (deg.)90.000, 98.110, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease H2 subunit A / RNase H2 subunit A / Aicardi-Goutieres syndrome 4 protein / AGS4 / RNase H(35) / Ribonuclease HI ...RNase H2 subunit A / Aicardi-Goutieres syndrome 4 protein / AGS4 / RNase H(35) / Ribonuclease HI large subunit / RNase HI large subunit / Ribonuclease HI subunit A


Mass: 33343.820 Da / Num. of mol.: 2 / Mutation: D34A, D169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH2A, RNASEHI, RNHIA / Plasmid: polycistronic construct based on pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: O75792, ribonuclease H
#2: Protein Ribonuclease H2 subunit B / RNase H2 subunit B / Aicardi-Goutieres syndrome 2 protein / AGS2 / Deleted in lymphocytic leukemia ...RNase H2 subunit B / Aicardi-Goutieres syndrome 2 protein / AGS2 / Deleted in lymphocytic leukemia 8 / Ribonuclease HI subunit B


Mass: 26699.691 Da / Num. of mol.: 2 / Fragment: RNASEH2B, UNP residues 2-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLEU8, RNASEH2B / Plasmid: polycistronic construct based on pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q5TBB1
#3: Protein Ribonuclease H2 subunit C / RNase H2 subunit C / Aicardi-Goutieres syndrome 3 protein / AGS3 / RNase H1 small subunit / ...RNase H2 subunit C / Aicardi-Goutieres syndrome 3 protein / AGS3 / RNase H1 small subunit / Ribonuclease HI subunit C


Mass: 17862.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AYP1, RNASEH2C / Plasmid: polycistronic construct based on pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q8TDP1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1M bis-Tris pH6.5, 0.2M KNO3, vapor diffusion, sitting drop, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.06→30 Å / Num. obs: 13282 / % possible obs: 98.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.18 / Χ2: 1.483 / Net I/σ(I): 3.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
4.06-4.253.50.6913390.87398.7
4.25-4.423.70.62212640.9398.6
4.42-4.623.70.46513331.02298.7
4.62-4.863.70.43412901.06198.1
4.86-5.163.90.37913121.14698.6
5.16-5.563.90.36313071.08498.8
5.56-6.1140.33213551.17698.8
6.11-6.994.20.2513411.44999
6.99-8.774.30.15413402.15798.5
8.77-304.10.07614013.38697.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
BUSTER2.9.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: re-refined PDB ID: 3KIO

3kio


Resolution: 4.06→30 Å / Cor.coef. Fo:Fc: 0.7988 / Cor.coef. Fo:Fc free: 0.7421 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.379 659 4.96 %RANDOM
Rwork0.3744 ---
obs0.3747 13281 --
Displacement parametersBiso max: 290.28 Å2 / Biso mean: 188.0547 Å2 / Biso min: 37.77 Å2
Baniso -1Baniso -2Baniso -3
1-54.7047 Å20 Å229.0948 Å2
2---27.6969 Å20 Å2
3----27.0078 Å2
Refine analyzeLuzzati coordinate error obs: 1.728 Å
Refinement stepCycle: LAST / Resolution: 4.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 0 0 0 7359
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d22902
X-RAY DIFFRACTIONt_trig_c_planes1132
X-RAY DIFFRACTIONt_gen_planes11515
X-RAY DIFFRACTIONt_it752720
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion10145
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_contact77284
X-RAY DIFFRACTIONt_bond_d752720.008
X-RAY DIFFRACTIONt_angle_deg1026720.96
X-RAY DIFFRACTIONt_omega_torsion1.48
X-RAY DIFFRACTIONt_other_torsion20.11
LS refinement shellResolution: 4.06→4.38 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2809 121 5.1 %
Rwork0.2846 2250 -
all0.2844 2371 -
obs-2371 -
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)
17.4175-2.57743.39127.6283-2.54314.94130.00750.12870.1977-0.17940.13370.0692-0.50860.4452-0.1412-0.3464-0.1290.1455-0.304-0.1719-0.2583147.88363.960680.9245
29.06941.2303-2.38035.0837-2.73524.59540.0289-0.0394-0.1168-0.036-0.17540.3699-0.0438-0.52990.1465-0.2359-0.165-0.13530.3040.08370.276494.4355-7.424764.1223
39.07073.1025-2.59626.5299-1.14147.5602-0.01130.334-0.3051-0.4421-0.06060.19630.4787-0.22980.0719-0.2838-0.0824-0.0905-0.2027-0.11570.0063117.6733-5.746263.2687
47.5025-2.58312.79468.3155-2.50349.12840.02960.20760.0678-0.27220.0905-0.011-0.3450.1348-0.1201-0.08110.1424-0.03810.304-0.13320.3009187.453314.6083171.6787
58.8654-0.003-1.89068.0048-2.94027.7655-0.0076-0.0505-0.1069-0.133-0.07990.22330.0601-0.42960.08750.0544-0.0194-0.18750.3040.04490.2556134.32613.2084156.2253
68.96171.3608-2.81448.3155-0.09737.4724-0.01870.1437-0.1615-0.1442-0.09670.14750.2627-0.15410.11540.11970.0921-0.07960.304-0.13370.2845157.6094.7655156.0047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A10 - 299
2X-RAY DIFFRACTION2{ B|* }B12 - 226
3X-RAY DIFFRACTION3{ C|* }C14 - 160
4X-RAY DIFFRACTION4{ D|* }D10 - 299
5X-RAY DIFFRACTION5{ E|* }E12 - 226
6X-RAY DIFFRACTION6{ F|* }F14 - 160

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