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- PDB-3puf: Crystal structure of human RNase H2 complex -

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Basic information

Entry
Database: PDB / ID: 3puf
TitleCrystal structure of human RNase H2 complex
Components
  • Ribonuclease H2 subunit A
  • Ribonuclease H2 subunit B
  • Ribonuclease H2 subunit C
KeywordsHYDROLASE / RNase H fold / triple barrel fold / RNase H
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 / RNA nuclease activity / 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 / mismatch repair / RNA nuclease activity / 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 / DNA replication / negative regulation of gene expression / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
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 ...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 / 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 A / Ribonuclease H2 subunit B / Ribonuclease H2 subunit C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFigiel, M. / Chon, H. / Cerritelli, S.M. / Cybulska, M. / Crouch, R.J. / Nowotny, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutieres syndrome defects.
Authors: Figiel, M. / Chon, H. / Cerritelli, S.M. / Cybulska, M. / Crouch, R.J. / Nowotny, M.
History
DepositionDec 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Nov 1, 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
G: Ribonuclease H2 subunit A
H: Ribonuclease H2 subunit B
I: Ribonuclease H2 subunit C
J: Ribonuclease H2 subunit A
K: Ribonuclease H2 subunit B
L: Ribonuclease H2 subunit C
M: Ribonuclease H2 subunit A
N: Ribonuclease H2 subunit B
O: Ribonuclease H2 subunit C
P: Ribonuclease H2 subunit A
Q: Ribonuclease H2 subunit B
R: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)465,89618
Polymers465,89618
Non-polymers00
Water1,63991
1
A: Ribonuclease H2 subunit A
B: Ribonuclease H2 subunit B
C: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)77,6493
Polymers77,6493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-63 kcal/mol
Surface area25710 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)77,6493
Polymers77,6493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-61 kcal/mol
Surface area25790 Å2
MethodPISA
3
G: Ribonuclease H2 subunit A
H: Ribonuclease H2 subunit B
I: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)77,6493
Polymers77,6493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-67 kcal/mol
Surface area27460 Å2
MethodPISA
4
J: Ribonuclease H2 subunit A
K: Ribonuclease H2 subunit B
L: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)77,6493
Polymers77,6493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-64 kcal/mol
Surface area25670 Å2
MethodPISA
5
M: Ribonuclease H2 subunit A
N: Ribonuclease H2 subunit B
O: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)77,6493
Polymers77,6493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-64 kcal/mol
Surface area25180 Å2
MethodPISA
6
P: Ribonuclease H2 subunit A
Q: Ribonuclease H2 subunit B
R: Ribonuclease H2 subunit C


Theoretical massNumber of molelcules
Total (without water)77,6493
Polymers77,6493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-62 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.068, 108.366, 114.264
Angle α, β, γ (deg.)105.90, 103.71, 111.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ribonuclease H2 subunit A / RNase H2A / RNase H2 subunit A / Aicardi-Goutieres syndrome 4 protein / AGS4 / RNase H(35) / ...RNase H2A / 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: 33724.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH2A, RNASEHI, RNHIA / Production host: Escherichia coli (E. coli) / References: UniProt: O75792, ribonuclease H
#2: Protein
Ribonuclease H2 subunit B / RNase H2B / RNase H2 subunit B / Aicardi-Goutieres syndrome 2 protein / AGS2 / Deleted in ...RNase H2B / RNase H2 subunit B / Aicardi-Goutieres syndrome 2 protein / AGS2 / Deleted in lymphocytic leukemia 8 / Ribonuclease HI subunit B


Mass: 25780.783 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH2B, DLEU8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TBB1, ribonuclease H
#3: Protein
Ribonuclease H2 subunit C / RNase H2C / RNase H2 subunit C / Aicardi-Goutieres syndrome 3 protein / AGS3 / RNase H1 small ...RNase H2C / RNase H2 subunit C / Aicardi-Goutieres syndrome 3 protein / AGS3 / RNase H1 small subunit / Ribonuclease HI subunit C


Mass: 18144.414 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH2C, AYP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDP1, ribonuclease H
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M MgCl2, 15% PEG 3350, 0.1M Bis-Tris (pH 5.5), and 2mM reduced glutathione, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 63130 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 69.09 Å2 / Rmerge(I) obs: 0.107
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.2 / % possible all: 87.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KIO

3kio


Resolution: 3.1→44.1 Å / Cor.coef. Fo:Fc: 0.9039 / Cor.coef. Fo:Fc free: 0.8611 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 3206 5.08 %RANDOM
Rwork0.203 ---
obs0.2057 62816 --
Displacement parametersBiso mean: 64.38 Å2
Baniso -1Baniso -2Baniso -3
1-4.1188 Å2-10.8887 Å28.0403 Å2
2--4.0317 Å2-2.3204 Å2
3----8.1505 Å2
Refine analyzeLuzzati coordinate error obs: 0.524 Å
Refinement stepCycle: LAST / Resolution: 3.1→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25729 0 0 91 25820
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.008263302
X-RAY DIFFRACTIONt_angle_deg1.03359782
X-RAY DIFFRACTIONt_dihedral_angle_d82692
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes4902
X-RAY DIFFRACTIONt_gen_planes39335
X-RAY DIFFRACTIONt_it2633020
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion22.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion35155
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_contact283824
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3079 236 5.61 %
Rwork0.235 3968 -
all0.2394 4204 -

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