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- PDB-8x21: HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV... -

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Basic information

Entry
Database: PDB / ID: 8x21
TitleHIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:ETV-TP ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • Pol protein (Fragment)
KeywordsTRANSFERASE / reverse transcriptase / HIV-1 / HBV / drug resistance / nucleoside analogue / entecavir
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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / 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
Chem-ET9 / DNA / DNA (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsYasutake, Y. / Hattori, S.I. / Mitsuya, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21fk0310113 Japan
CitationJournal: Sci Rep / Year: 2024
Title: Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations.
Authors: Yasutake, Y. / Hattori, S.I. / Kumamoto, H. / Tamura, N. / Maeda, K. / Mitsuya, H.
History
DepositionNov 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)256,84616
Polymers255,2116
Non-polymers1,63610
Water8,251458
1
A: Pol protein (Fragment)
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4238
Polymers127,6053
Non-polymers8185
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12180 Å2
ΔGint-42 kcal/mol
Surface area46440 Å2
MethodPISA
2
C: Pol protein (Fragment)
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4238
Polymers127,6053
Non-polymers8185
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-44 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.447, 284.447, 95.728
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 Pol protein (Fragment)


Mass: 64019.363 Da / Num. of mol.: 2 / Mutation: L74V, Y115F, F116Y, Q151M, C162S, C280S
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
#2: Protein HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT


Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C162S, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 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: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 468 molecules

#4: Chemical ChemComp-ET9 / [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate / Entecavir 5'-triphosphate


Mass: 517.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: bis-tris-HCl, di-ammonium hydrogen citrate, MgCl2, PEG6000, 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: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 123410 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 49.3 Å2 / Rrim(I) all: 0.157 / Net I/σ(I): 7.4
Reflection shellResolution: 2.33→2.37 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6116 / Rrim(I) all: 0.875

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Processing

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

6kdn


Resolution: 2.33→48.666 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 6262 5.07 %
Rwork0.1754 --
obs0.1775 123407 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→48.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15688 1495 102 458 17743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01217890
X-RAY DIFFRACTIONf_angle_d1.17924605
X-RAY DIFFRACTIONf_dihedral_angle_d24.0886846
X-RAY DIFFRACTIONf_chiral_restr0.0672662
X-RAY DIFFRACTIONf_plane_restr0.0072835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.35650.31982040.25083931X-RAY DIFFRACTION100
2.3565-2.38420.28361970.23263935X-RAY DIFFRACTION100
2.3842-2.41330.2821920.22993916X-RAY DIFFRACTION100
2.4133-2.44390.28222260.23033859X-RAY DIFFRACTION100
2.4439-2.4760.26892320.2313895X-RAY DIFFRACTION100
2.476-2.50990.33832170.22683887X-RAY DIFFRACTION100
2.5099-2.54580.29222070.2243911X-RAY DIFFRACTION100
2.5458-2.58380.26772130.21663883X-RAY DIFFRACTION100
2.5838-2.62420.26281930.21353922X-RAY DIFFRACTION100
2.6242-2.66720.26022130.19653929X-RAY DIFFRACTION100
2.6672-2.71320.23531790.20083919X-RAY DIFFRACTION100
2.7132-2.76250.26232100.19943872X-RAY DIFFRACTION100
2.7625-2.81560.2342100.19933939X-RAY DIFFRACTION100
2.8156-2.87310.27182360.20653853X-RAY DIFFRACTION100
2.8731-2.93550.28312100.20973937X-RAY DIFFRACTION100
2.9355-3.00380.2462300.20073886X-RAY DIFFRACTION100
3.0038-3.07890.2592080.19633849X-RAY DIFFRACTION100
3.0789-3.16220.24132040.18353947X-RAY DIFFRACTION100
3.1622-3.25520.25862260.18643882X-RAY DIFFRACTION100
3.2552-3.36020.22411810.17733905X-RAY DIFFRACTION100
3.3602-3.48030.21942290.17733925X-RAY DIFFRACTION100
3.4803-3.61960.24842060.1753882X-RAY DIFFRACTION100
3.6196-3.78430.19941910.17253944X-RAY DIFFRACTION100
3.7843-3.98370.18812320.15773871X-RAY DIFFRACTION100
3.9837-4.23320.18982230.14843886X-RAY DIFFRACTION100
4.2332-4.55980.15811940.14173924X-RAY DIFFRACTION100
4.5598-5.01830.17662040.14183913X-RAY DIFFRACTION100
5.0183-5.74340.19912030.16173899X-RAY DIFFRACTION100
5.7434-7.23230.20292050.1753916X-RAY DIFFRACTION100
7.2323-48.6660.18351870.16153928X-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)
10.7769-0.0264-0.25420.39750.05492.3885-0.0687-0.06940.0790.00340.0264-0.07040.10170.06790.02860.2664-0.00160.03270.3551-0.03150.3947178.2978275.8742-146.3126
22.31260.38640.18130.81260.40471.5572-0.14490.16090.2372-0.142-0.06570.3436-0.1698-0.63950.17570.30220.0587-0.04570.609-0.0230.5111146.0984276.6335-155.3331
31.01840.61210.55764.44223.2925.3203-0.1632-0.1996-0.2347-0.2056-0.07220.2190.2377-0.4560.20890.3262-0.0370.06320.42160.00720.369174.7921264.6748-147.9232
41.54420.0992-0.15771.2629-0.41470.9897-0.06470.14280.1732-0.15650.07390.0945-0.0583-0.0595-0.01920.2781-0.04260.01980.35990.00760.3232211.2994282.0273-183.0736
50.6121-0.39910.05981.7671-0.78171.0490.00850.05090.0673-0.1045-0.0103-0.07530.04660.25570.01150.315-0.03780.04980.4780.010.3955238.788262.7723-181.9179
63.81840.34260.31512.303-0.48092.7410.13960.5097-0.2387-0.2701-0.3622-0.14290.45450.14420.22390.4408-0.01730.06910.4341-0.01060.3125207.5314274.0244-191.0426
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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