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- PDB-3bsu: Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA -

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Basic information

Entry
Database: PDB / ID: 3bsu
TitleHybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA
Components
  • DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')
  • RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
  • Ribonuclease H1
KeywordsHYDROLASE/RNA/DNA / RNase H / RNA/DNA hybrid / dsRNA / HYDROLASE-RNA-DNA COMPLEX
Function / homology
Function and homology information


DNA replication, removal of RNA primer / RNA catabolic process / ribonuclease H / RNA nuclease activity / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease H1, N-terminal domain / Ribonuclease H1, eukaryote / Ribonuclease HI; Chain A / : / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribosomal protein L9/RNase H1, N-terminal / RNase H / RNase H type-1 domain profile. ...Ribonuclease H1, N-terminal domain / Ribonuclease H1, eukaryote / Ribonuclease HI; Chain A / : / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribosomal protein L9/RNase H1, N-terminal / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Ribonuclease H1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNowotny, M. / Cerritelli, S.M. / Ghirlando, R. / Gaidamakov, S.A. / Crouch, R.J. / Yang, W.
CitationJournal: Embo J. / Year: 2008
Title: Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
Authors: Nowotny, M. / Cerritelli, S.M. / Ghirlando, R. / Gaidamakov, S.A. / Crouch, R.J. / Yang, W.
History
DepositionDec 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
E: DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')
I: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
J: DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')
A: Ribonuclease H1
B: Ribonuclease H1
C: Ribonuclease H1
F: Ribonuclease H1
G: Ribonuclease H1
H: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,40412
Polymers52,35610
Non-polymers492
Water4,540252
1
D: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
E: DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')
A: Ribonuclease H1
B: Ribonuclease H1
C: Ribonuclease H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2267
Polymers26,1785
Non-polymers492
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')
J: DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')
F: Ribonuclease H1
G: Ribonuclease H1
H: Ribonuclease H1


Theoretical massNumber of molelcules
Total (without water)26,1785
Polymers26,1785
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.492, 64.262, 140.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')


Mass: 3772.296 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')


Mass: 3814.298 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
Ribonuclease H1 / E.C.3.1.26.4 / RNase H1 / Ribonuclease H type II


Mass: 6197.077 Da / Num. of mol.: 6 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEH1, RNH1 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: O60930, ribonuclease H
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2 M NaCl, 0.1 M HEPES (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCl11
2Hepes11
3NaCl12
4Hepes12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 24814 / Num. obs: 23892 / % possible obs: 96.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.9 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2360 -random
Rwork0.22 ---
all-24814 --
obs-23892 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 1033 2 252 3743
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009515
X-RAY DIFFRACTIONc_angle_deg1.26951
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.4271.5
X-RAY DIFFRACTIONc_mcangle_it2.2932
X-RAY DIFFRACTIONc_scbond_it1.9422
X-RAY DIFFRACTIONc_scangle_it2.7932.5

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