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- PDB-3v1q: Crystal structures of the reverse transcriptase-associated ribonu... -

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Basic information

Entry
Database: PDB / ID: 3v1q
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


virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 P30 core shell protein ...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. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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: 2 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H p80


Theoretical massNumber of molelcules
Total (without water)18,1391
Polymers18,1391
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.530, 37.530, 99.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Reverse transcriptase/ribonuclease H p80


Mass: 18138.512 Da / Num. of mol.: 1 / Fragment: RNase H domain (UNP residues 1155-1328)
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.94 Å3/Da / Density % sol: 36.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 40% PEG1500, 5 mM magnesium chloride, 100 mM sodium citrate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jul 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: 2→20 Å / Num. all: 9390 / Num. obs: 9361 / % possible obs: 99.7 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 7.5 % / Rmerge(I) obs: 0.146
Reflection shellResolution: 2→2.3 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.71 / Num. unique all: 3191 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.443 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 747 8 %RANDOM
Rwork0.1692 ---
obs0.1715 9334 99.91 %-
all-9361 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.387 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.608 Å2-0 Å20 Å2
2---0.608 Å2-0 Å2
3---2.7704 Å2
Refinement stepCycle: LAST / Resolution: 2→18.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1206 0 0 80 1286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151228
X-RAY DIFFRACTIONf_angle_d1.5611661
X-RAY DIFFRACTIONf_dihedral_angle_d15.463456
X-RAY DIFFRACTIONf_chiral_restr0.113186
X-RAY DIFFRACTIONf_plane_restr0.008218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.15430.26281480.24611711X-RAY DIFFRACTION100
2.1543-2.37060.24061490.21111713X-RAY DIFFRACTION100
2.3706-2.71270.25141500.18261722X-RAY DIFFRACTION100
2.7127-3.41420.21411490.16521710X-RAY DIFFRACTION100
3.4142-18.44330.15321510.14451731X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.8876 Å / Origin y: 10.4595 Å / Origin z: -6.0221 Å
111213212223313233
T0.1208 Å20.0139 Å20.0157 Å2-0.1217 Å2-0.0133 Å2--0.0959 Å2
L0.8753 °20.7073 °20.3371 °2-2.3617 °20.1795 °2--0.4447 °2
S0.0161 Å °0.0503 Å °-0.1068 Å °-0.0322 Å °0.0136 Å °-0.0424 Å °-0.0261 Å °0.0384 Å °0 Å °
Refinement TLS groupSelection details: all

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