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- PDB-7aid: HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND D-ASPARTATE TENOFOVIR -

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Basic information

Entry
Database: PDB / ID: 7aid
TitleHIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND D-ASPARTATE TENOFOVIR
Components
  • (Gag-Pol polyprotein) 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 tenofovir 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 / 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 / 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 / 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
D-Aspartate Tenofovir / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsGu, W. / Martinez, S.E. / Nguyen, H. / Xu, H. / Herdewijn, P. / de Jonghe, S. / Das, K.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues.
Authors: Gu, W. / Martinez, S. / Nguyen, H. / Xu, H. / Herdewijn, P. / De Jonghe, S. / Das, K.
History
DepositionSep 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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: Gag-Pol polyprotein
B: Gag-Pol polyprotein
C: Gag-Pol polyprotein
D: Gag-Pol polyprotein
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')
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,2419
Polymers257,8398
Non-polymers4021
Water1,09961
1
A: Gag-Pol polyprotein
B: Gag-Pol polyprotein
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')


Theoretical massNumber of molelcules
Total (without water)128,9204
Polymers128,9204
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-46 kcal/mol
Surface area49240 Å2
MethodPISA
2
C: Gag-Pol polyprotein
D: Gag-Pol polyprotein
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3225
Polymers128,9204
Non-polymers4021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-46 kcal/mol
Surface area49230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.861, 133.461, 140.230
Angle α, β, γ (deg.)90.000, 98.350, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Gag-Pol polyprotein / Pr160Gag-Pol


Mass: 64022.414 Da / Num. of mol.: 2 / Mutation: Q258C, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Protein Gag-Pol polyprotein / Pr160Gag-Pol


Mass: 50039.488 Da / Num. of mol.: 2 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 4 molecules TEPF

#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 , 2 types, 62 molecules

#5: Chemical ChemComp-REK / D-Aspartate Tenofovir / (2~{R})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]butanedioic acid


Mass: 402.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N6O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Description: long parallelogram with width greater than thickness
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
PH range: pH 8.3 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.15→53.37 Å / Num. obs: 56199 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 87.72 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.104 / Net I/σ(I): 5.4
Reflection shellResolution: 3.15→3.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.684 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4634 / CC1/2: 0.289 / Rpim(I) all: 0.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MxCuBEdata collection
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHENIX1.17.1phasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V4I

3v4i


Resolution: 3.15→53.37 Å / SU ML: 0.4889 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 1630 2.9 %
Rwork0.2139 54487 -
obs0.215 56117 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.71 Å2
Refinement stepCycle: LAST / Resolution: 3.15→53.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15835 1761 27 61 17684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001918265
X-RAY DIFFRACTIONf_angle_d0.429525174
X-RAY DIFFRACTIONf_chiral_restr0.03932740
X-RAY DIFFRACTIONf_plane_restr0.00312871
X-RAY DIFFRACTIONf_dihedral_angle_d14.85857009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.240.36831380.34924531X-RAY DIFFRACTION98.77
3.24-3.350.3341530.30574523X-RAY DIFFRACTION98.82
3.35-3.470.33251330.28384476X-RAY DIFFRACTION98.63
3.47-3.610.29371360.26384517X-RAY DIFFRACTION98.58
3.61-3.770.29111540.24814489X-RAY DIFFRACTION99.17
3.77-3.970.27811230.23744544X-RAY DIFFRACTION99.13
3.97-4.220.27221270.2034577X-RAY DIFFRACTION99.24
4.22-4.540.21781450.19344502X-RAY DIFFRACTION98.77
4.54-50.23881310.1894574X-RAY DIFFRACTION99.01
5-5.720.21341290.19234560X-RAY DIFFRACTION99.36
5.72-7.210.25241240.21524567X-RAY DIFFRACTION98.78
7.21-53.370.2011370.17214627X-RAY DIFFRACTION98.53

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