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- PDB-7dbn: HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V/F160M:... -

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Basic information

Entry
Database: PDB / ID: 7dbn
TitleHIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V/F160M:DNA:dCTP ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • HIV-1 reverse transcriptase p66 subunit
KeywordsTRANSFERASE/DNA / Entecavir 5'-triphosphate / HIV-1 / HBV / reverse transcriptase / drug resistance / TRANSFERASE-DNA complex / REPLICATION
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus type 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsYasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20fk0310113 Japan
CitationJournal: J.Virol. / Year: 2021
Title: Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations.
Authors: Nakajima, S. / Watashi, K. / Kato, T. / Muramatsu, M. / Wakita, T. / Tamura, N. / Hattori, S.I. / Maeda, K. / Mitsuya, H. / Yasutake, Y. / Toyoda, T.
History
DepositionOct 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,57414
Polymers255,2236
Non-polymers1,3518
Water3,279182
1
A: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2877
Polymers127,6113
Non-polymers6764
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-49 kcal/mol
Surface area46660 Å2
MethodPISA
2
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2877
Polymers127,6113
Non-polymers6764
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-52 kcal/mol
Surface area47240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.681, 285.681, 96.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HIV-1 reverse transcriptase p66 subunit


Mass: 63985.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: D3XFN5, RNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT


Mass: 51861.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain DNA/RNA (38-MER)


Mass: 11764.525 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 190 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 83121 / % possible obs: 100 % / Redundancy: 5.4 % / Rrim(I) all: 0.089 / Net I/σ(I): 14.8
Reflection shellResolution: 2.67→2.72 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4525 / Rrim(I) all: 0.982

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KDJ

6kdj


Resolution: 2.67→48.895 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 4204 5.06 %
Rwork0.1767 --
obs0.1791 83103 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→48.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15682 1501 82 182 17447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717861
X-RAY DIFFRACTIONf_angle_d0.93224568
X-RAY DIFFRACTIONf_dihedral_angle_d24.7396817
X-RAY DIFFRACTIONf_chiral_restr0.1152667
X-RAY DIFFRACTIONf_plane_restr0.0052829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6701-2.70040.38551250.32542X-RAY DIFFRACTION99
2.7004-2.73220.3441150.28342665X-RAY DIFFRACTION100
2.7322-2.76550.34531470.27212660X-RAY DIFFRACTION100
2.7655-2.80050.29461340.25462643X-RAY DIFFRACTION100
2.8005-2.83740.30091460.24142606X-RAY DIFFRACTION100
2.8374-2.87620.2961540.23742608X-RAY DIFFRACTION100
2.8762-2.91730.32671400.22412662X-RAY DIFFRACTION100
2.9173-2.96080.30661610.22392593X-RAY DIFFRACTION100
2.9608-3.00710.28711550.21512626X-RAY DIFFRACTION100
3.0071-3.05640.26611550.21852615X-RAY DIFFRACTION100
3.0564-3.10910.28631370.21372680X-RAY DIFFRACTION100
3.1091-3.16560.23571270.20862632X-RAY DIFFRACTION100
3.1656-3.22650.29491570.20832591X-RAY DIFFRACTION100
3.2265-3.29230.24731340.1862625X-RAY DIFFRACTION100
3.2923-3.36390.22311230.18562665X-RAY DIFFRACTION100
3.3639-3.44210.24091570.17812619X-RAY DIFFRACTION100
3.4421-3.52820.21641420.18272639X-RAY DIFFRACTION100
3.5282-3.62360.26571340.17842605X-RAY DIFFRACTION100
3.6236-3.73020.24591370.17332658X-RAY DIFFRACTION100
3.7302-3.85050.20611300.16872639X-RAY DIFFRACTION100
3.8505-3.98810.22431670.16832592X-RAY DIFFRACTION100
3.9881-4.14770.20551430.15352642X-RAY DIFFRACTION100
4.1477-4.33630.21141350.15152625X-RAY DIFFRACTION100
4.3363-4.56480.19011460.15032645X-RAY DIFFRACTION100
4.5648-4.85050.18631300.15162626X-RAY DIFFRACTION100
4.8505-5.22470.16821420.14462650X-RAY DIFFRACTION100
5.2247-5.74970.20611380.16212624X-RAY DIFFRACTION100
5.7497-6.580.20121310.172633X-RAY DIFFRACTION100
6.58-8.28360.18121520.16012621X-RAY DIFFRACTION100
8.2836-48.8950.18671100.162668X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.29530.0325-0.53790.69460.07762.7111-0.0927-0.13830.10310.02460.0499-0.11990.18010.13230.0210.26180.01470.03060.3981-0.05750.371178.9708276.8759-147.1126
23.27930.710.43671.2090.72012.2762-0.18260.19870.3678-0.2015-0.05890.4378-0.2247-0.77040.20390.34560.0751-0.06050.6503-0.04490.5092146.7349277.7684-156.1896
32.0550.19630.36545.05682.75845.5416-0.1643-0.3744-0.3329-0.09560.02360.27810.3852-0.49850.15190.3529-0.04050.06240.48960.01250.3261175.5861265.8188-148.6898
42.10940.0451-0.23231.5002-0.49721.1402-0.0470.24560.1524-0.20040.0580.1118-0.0659-0.0866-0.0120.3279-0.05050.02890.4344-0.00810.3178212.2088283.1855-184.2161
51.018-0.48550.09782.5319-0.89971.2805-0.00320.064-0.0108-0.037-0.0383-0.15670.0420.31490.04540.2761-0.05180.04130.47690.01610.3792239.8342263.9462-183.0254
64.59441.04170.14992.6806-0.71383.71120.14570.6718-0.4457-0.3119-0.3836-0.23380.54450.18420.25810.461-0.01320.08290.5305-0.05390.3631208.4243275.2181-192.2141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 1 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 5 through 427)
6X-RAY DIFFRACTION6(chain 'F' and resid -4 through 33)

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