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- PDB-4zhr: Structure of HIV-1 RT Q151M mutant -

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Basic information

Entry
Database: PDB / ID: 4zhr
TitleStructure of HIV-1 RT Q151M mutant
Components
  • RT p51 subunit
  • RT p66 subunit
KeywordsTRANSFERASE / HIV-1 reverse transcriptase / closed conformation / Q151M
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / 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 / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Retrovirus capsid, C-terminal / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsNakamura, A. / Tamura, N. / Yasutake, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Health, Labour and Welfare Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the HIV-1 reverse transcriptase Q151M mutant: insights into the inhibitor resistance of HIV-1 reverse transcriptase and the structure of the nucleotide-binding pocket of Hepatitis B virus polymerase.
Authors: Nakamura, A. / Tamura, N. / Yasutake, Y.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RT p66 subunit
B: RT p51 subunit


Theoretical massNumber of molelcules
Total (without water)115,9412
Polymers115,9412
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-33 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.737, 145.737, 118.395
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein RT p66 subunit


Mass: 64677.332 Da / Num. of mol.: 1 / Mutation: Q151M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pCDF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
References: UniProt: P12497*PLUS, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein RT p51 subunit


Mass: 51264.039 Da / Num. of mol.: 1 / Mutation: T215I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
References: UniProt: P12497*PLUS, RNA-directed DNA polymerase, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe gene encoding HIV-1 RT used in this study is originated from the HIV-1 clone pNL4-3 (GenBank ...The gene encoding HIV-1 RT used in this study is originated from the HIV-1 clone pNL4-3 (GenBank ID, M19921.2).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 9% PEG 8000, 0.2M imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 44912 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTH

1rth


Resolution: 2.601→47.704 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 2258 5.03 %
Rwork0.2031 --
obs0.2049 44866 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→47.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7871 0 0 38 7909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028085
X-RAY DIFFRACTIONf_angle_d0.54110980
X-RAY DIFFRACTIONf_dihedral_angle_d10.9953063
X-RAY DIFFRACTIONf_chiral_restr0.0221189
X-RAY DIFFRACTIONf_plane_restr0.0031382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.65760.33811400.30442596X-RAY DIFFRACTION99
2.6576-2.71940.31351350.28262634X-RAY DIFFRACTION100
2.7194-2.78740.34131370.27582627X-RAY DIFFRACTION100
2.7874-2.86280.34471370.25672661X-RAY DIFFRACTION100
2.8628-2.9470.28651320.27052631X-RAY DIFFRACTION100
2.947-3.04210.29351540.26072643X-RAY DIFFRACTION100
3.0421-3.15080.32981370.26312644X-RAY DIFFRACTION100
3.1508-3.27690.33581510.25832654X-RAY DIFFRACTION100
3.2769-3.4260.32231370.25412645X-RAY DIFFRACTION100
3.426-3.60660.25861610.24482646X-RAY DIFFRACTION100
3.6066-3.83250.26691440.22262660X-RAY DIFFRACTION100
3.8325-4.12820.24341250.19652654X-RAY DIFFRACTION100
4.1282-4.54340.20611400.17642692X-RAY DIFFRACTION100
4.5434-5.20010.19921460.16812686X-RAY DIFFRACTION100
5.2001-6.54890.21331520.18952709X-RAY DIFFRACTION100
6.5489-47.71160.15551300.14882826X-RAY DIFFRACTION99

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