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- PDB-7ot6: HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND inhibitor RMC-282 -

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Basic information

Entry
Database: PDB / ID: 7ot6
TitleHIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND inhibitor RMC-282
Components
  • (Reverse transcriptase/ribonuclease ...) x 2
  • DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
  • DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)*CP*GP*CP*CP*(DDG))-3')
KeywordsTRANSFERASE / REVERSE TRANSCRIPTASE / RT INHIBITOR COMPLEX / ACYCLIC NUCLEOSIDE PHOSPHONATE ANALOG / RT-DNA COMPLEX
Function / homology
Function and homology information


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 ...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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-1I4 / 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 9, 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

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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(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
F: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)*CP*GP*CP*CP*(DDG))-3')
P: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)*CP*GP*CP*CP*(DDG))-3')
T: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,59510
Polymers257,2138
Non-polymers3832
Water00
1
C: Reverse transcriptase/ribonuclease H
D: Reverse transcriptase/ribonuclease H
E: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
F: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)*CP*GP*CP*CP*(DDG))-3')


Theoretical massNumber of molelcules
Total (without water)128,6064
Polymers128,6064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12990 Å2
ΔGint-49 kcal/mol
Surface area48790 Å2
MethodPISA
2
A: Reverse transcriptase/ribonuclease H
B: Reverse transcriptase/ribonuclease H
P: DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)*CP*GP*CP*CP*(DDG))-3')
T: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9896
Polymers128,6064
Non-polymers3832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-53 kcal/mol
Surface area49030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.447, 132.679, 139.717
Angle α, β, γ (deg.)90.000, 98.510, 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(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*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)*CP*GP*CP*CP*(DDG))-3')


Mass: 6161.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-1I4 / (R)-N-(1-(6-amino-9H-purin-9-yl)propan-2-yl)-N-(2-phosphonoethyl)glycine


Mass: 358.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N6O5P / Feature type: SUBJECT OF INVESTIGATION

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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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16-19.5% 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: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.2→95.7 Å / Num. obs: 53347 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 91.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.074 / Net I/σ(I): 7.5
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.685 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4601 / CC1/2: 0.275 / Rpim(I) all: 0.722 / % possible all: 100

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Processing

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

3v4i


Resolution: 3.2→95.7 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 1601 3 %
Rwork0.2233 51710 -
obs0.2244 53311 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 294.05 Å2 / Biso mean: 117.5471 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.2→95.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15816 1757 46 0 17619
Biso mean--148.23 --
Num. residues----2020
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
3.2-3.30.41181340.372146704804
3.3-3.420.40431540.334446614815
3.42-3.560.3331480.307547064854
3.56-3.720.34511430.272546684811
3.72-3.920.28261460.255146784824
3.92-4.160.26211440.226946894833
4.16-4.480.2511460.208547074853
4.48-4.930.24311450.204246964841
4.93-5.650.28611460.209147164862
5.65-7.120.27921460.229747224868
7.12-95.70.17011490.1747974946

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