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- PDB-7out: HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND INHIBITOR RMC-264 -

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Basic information

Entry
Database: PDB / ID: 7out
TitleHIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND INHIBITOR RMC-264
Components
  • (Reverse transcriptase/ribonuclease ...) x 2
  • DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3')
  • DNA (5'-D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3')
KeywordsTRANSFERASE / REVERSE TRANSCRIPTASE / RT INHIBITOR COMPLEX / ACYCLIC NUCLEOSIDE PHOSPHONATE ANALOG / RT-DNA COMPLEX
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / 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-1KK / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus type 1 BH10
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMartinez, S.E. / Singh, A.K. / Gu, W. / Das, K.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design.
Authors: Gu, W. / Martinez, S. / Singh, A.K. / Nguyen, H. / Rozenski, J. / Schols, D. / Herdewijn, P. / Das, K. / De Jonghe, S.
History
DepositionJun 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Reverse transcriptase/ribonuclease H
D: Reverse transcriptase/ribonuclease H
A: Reverse transcriptase/ribonuclease H
B: Reverse transcriptase/ribonuclease H
E: DNA (5'-D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3')
F: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3')
T: DNA (5'-D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,20910
Polymers257,8398
Non-polymers3702
Water181
1
C: Reverse transcriptase/ribonuclease H
D: Reverse transcriptase/ribonuclease H
E: DNA (5'-D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3')
F: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3')


Theoretical massNumber of molelcules
Total (without water)128,9204
Polymers128,9204
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12990 Å2
ΔGint-47 kcal/mol
Surface area48920 Å2
MethodPISA
2
A: Reverse transcriptase/ribonuclease H
B: Reverse transcriptase/ribonuclease H
T: DNA (5'-D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,2896
Polymers128,9204
Non-polymers3702
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13460 Å2
ΔGint-56 kcal/mol
Surface area49210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.597, 132.579, 139.419
Angle α, β, γ (deg.)90.000, 98.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Reverse transcriptase/ribonuclease ... , 2 types, 4 molecules CADB

#1: Protein Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT


Mass: 64022.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus RIL
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein Reverse transcriptase/ribonuclease H / Exoribonuclease H / p51 RT


Mass: 50039.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus RIL
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H

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DNA chain , 2 types, 4 molecules ETFP

#3: DNA chain DNA (5'-D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*G)-3')


Mass: 8383.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus type 1 BH10
#4: DNA chain DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(DDG))-3')


Mass: 6474.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 3 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-1KK / (S)-2-(3-(6-amino-9H-purin-9-yl)propoxy)-3-phosphonopropanoic acid


Mass: 345.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N5O6P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16-19% V/V PEG SMEAR BROAD, 0.2 M (NH4)2SO4, 0.1 M TRIS-HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.2→53.81 Å / Num. obs: 53240 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 116.05 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.059 / Rrim(I) all: 0.147 / Net I/σ(I): 7.8 / Num. measured all: 322541 / Scaling rejects: 138
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6 % / Rmerge(I) obs: 2.097 / Num. unique obs: 4595 / CC1/2: 0.328 / Rpim(I) all: 0.922 / Rrim(I) all: 2.295 / % possible all: 100

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHENIX1.19.1_4122refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V4I

3v4i


Resolution: 3.2→53.81 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1567 2.95 %
Rwork0.2194 51623 -
obs0.2208 53190 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 369.28 Å2 / Biso mean: 145.0809 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.2→53.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15819 1778 24 1 17622
Biso mean--247.68 30 -
Num. residues----2021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2-3.30.41951260.361946544780
3.3-3.420.36651400.341446774817
3.42-3.560.37851400.31446894829
3.56-3.720.3381440.264746634807
3.72-3.920.29211470.248246794826
3.92-4.160.29171410.230246724813
4.16-4.480.26131440.208747024846
4.48-4.930.20821470.19746834830
4.93-5.650.23591440.207147094853
5.65-7.110.28411450.23347064851
7.11-53.810.2291490.176647894938

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