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- PDB-3v1o: Crystal structures of the reverse transcriptase-associated ribonu... -

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Entry
Database: PDB / ID: 3v1o
TitleCrystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus
ComponentsReverse transcriptase/ribonuclease H p80
KeywordsHYDROLASE / Reverse Transcription
Function / homology
Function and homology information


ribonuclease H / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...ribonuclease H / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / : / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / : / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesXenotropic MuLV-related virus VP35
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.876 Å
AuthorsZhou, D. / Wlodawer, A.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus.
Authors: Zhou, D. / Chung, S. / Miller, M. / Le Grice, S.F. / Wlodawer, A.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H p80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4697
Polymers19,8741
Non-polymers5956
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.290, 84.219, 70.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2-

SO4

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Components

#1: Protein Reverse transcriptase/ribonuclease H p80


Mass: 19874.469 Da / Num. of mol.: 1 / Fragment: RNase H domain (UNP residues 1154-1328)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenotropic MuLV-related virus VP35 / Gene: gag-pol, POL_XMRV3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2F7J3, ribonuclease H
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 38.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% PEG3000, 15% MPD, 2% isopropanol, 0.2 M lithium sulfate, 0.1 M imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.876→45.032 Å / Num. obs: 11792 / % possible obs: 89.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.079
Reflection shellResolution: 1.876→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.5 / Num. unique all: 743 / % possible all: 57.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.876→27.763 Å / SU ML: 0.5 / σ(F): 1.36 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 815 6.93 %RANDOM
Rwork0.1728 ---
obs0.1761 11760 88.12 %-
all-11792 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.374 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.892 Å20 Å2-0 Å2
2--22.1371 Å20 Å2
3----11.2451 Å2
Refinement stepCycle: LAST / Resolution: 1.876→27.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 34 71 1383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011328
X-RAY DIFFRACTIONf_angle_d1.2651795
X-RAY DIFFRACTIONf_dihedral_angle_d13.734491
X-RAY DIFFRACTIONf_chiral_restr0.09196
X-RAY DIFFRACTIONf_plane_restr0.007230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.876-1.99360.2526810.21161084X-RAY DIFFRACTION53
1.9936-2.14750.24231120.17281643X-RAY DIFFRACTION81
2.1475-2.36350.24491450.17071951X-RAY DIFFRACTION96
2.3635-2.70520.20661400.16792052X-RAY DIFFRACTION100
2.7052-3.40730.21871580.16252078X-RAY DIFFRACTION100
3.4073-27.76650.20581790.17632137X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.6138 Å / Origin y: 25.9261 Å / Origin z: 1.5326 Å
111213212223313233
T0.1048 Å2-0.0198 Å20.0067 Å2-0.1333 Å20.0095 Å2--0.1329 Å2
L3.2593 °2-0.6278 °2-0.0723 °2-2.1607 °2-0.0393 °2--3.1869 °2
S-0.0109 Å °-0.0738 Å °0.1536 Å °0.0659 Å °0.0827 Å °0.0513 Å °-0.2077 Å °0.076 Å °-0.0544 Å °
Refinement TLS groupSelection details: all

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