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- PDB-7lpx: Crystal Structure of HIV-1 RT in Complex with NBD-14270 -

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Basic information

Entry
Database: PDB / ID: 7lpx
TitleCrystal Structure of HIV-1 RT in Complex with NBD-14270
Components
  • Reverse transcriptase p51
  • Reverse transcriptase p66
KeywordsTRANSFERASE/INHIBITOR / Human immunodeficiency virus 1 / non nucleotide-reverse transcriptase inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR 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-YB7 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLosada, N. / Ruiz, F.X. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)MERIT Award R37 AI027690 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites.
Authors: Losada, N. / Ruiz, F.X. / Curreli, F. / Gruber, K. / Pilch, A. / Das, K. / Debnath, A.K. / Arnold, E.
History
DepositionFeb 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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
A: Reverse transcriptase p66
B: Reverse transcriptase p51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8957
Polymers114,0862
Non-polymers8105
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: 1 biological assembly in the asymmetric unit: A,B
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-99 kcal/mol
Surface area47230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.597, 73.065, 107.397
Angle α, β, γ (deg.)90.000, 100.115, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Reverse transcriptase p66


Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein Reverse transcriptase p51


Mass: 50096.539 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-YB7 / ~{N}-[(1~{S})-2-azanyl-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-3-methyl-5-[5-(trifluoromethyl)pyridin-2-yl]-1~{H}-pyrrole-2-carboxamide


Mass: 425.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18F3N5O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 10% PEG 8,000, 4% PEG 400, 100 mM imidazole pH 6.6,10 mM spermine, 15 mM MgSO4,100 mM (NH4)2SO4, and 5 mM tris(2-carboxyethyl)phosphine(TCEP)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.96868 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96868 Å / Relative weight: 1
ReflectionResolution: 2.448→30.31 Å / Num. obs: 45373 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 69.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Rrim(I) all: 0.073 / Net I/σ(I): 23.6
Reflection shellResolution: 2.448→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2165 / CC1/2: 0.242 / Rpim(I) all: 0.42 / Rrim(I) all: 0.79 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIXdev_3051refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q


Resolution: 2.45→30.31 Å / SU ML: 0.4253 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.5692 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2504 1998 4.41 %
Rwork0.2149 43341 -
obs0.2165 45339 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.14 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7925 0 49 129 8103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068187
X-RAY DIFFRACTIONf_angle_d0.969511132
X-RAY DIFFRACTIONf_chiral_restr0.05911203
X-RAY DIFFRACTIONf_plane_restr0.00541397
X-RAY DIFFRACTIONf_dihedral_angle_d20.90033088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.42841330.35552888X-RAY DIFFRACTION94.23
2.51-2.580.31121410.33013066X-RAY DIFFRACTION98.68
2.58-2.650.37181430.30543078X-RAY DIFFRACTION99.41
2.65-2.740.3171420.29273086X-RAY DIFFRACTION99.72
2.74-2.840.31041430.27963117X-RAY DIFFRACTION99.88
2.84-2.950.30071440.25713096X-RAY DIFFRACTION99.57
2.95-3.080.30381400.2553051X-RAY DIFFRACTION99.78
3.08-3.250.29551440.25783116X-RAY DIFFRACTION99.72
3.25-3.450.26571430.23973117X-RAY DIFFRACTION99.82
3.45-3.710.26241440.22523123X-RAY DIFFRACTION99.97
3.71-4.090.27131440.20843105X-RAY DIFFRACTION99.91
4.09-4.680.21641450.18453150X-RAY DIFFRACTION100
4.68-5.890.21761450.1983143X-RAY DIFFRACTION99.94
5.89-30.310.21491470.18093205X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: 202.757499437 Å / Origin y: 0.32219918158 Å / Origin z: 28.6467104973 Å
111213212223313233
T0.462503727109 Å2-0.0318712977394 Å20.0855686339168 Å2-0.435818333147 Å20.00488595213856 Å2--0.517719478919 Å2
L0.672652538838 °2-0.338978772196 °20.785536962959 °2-0.674026323397 °2-0.485920972997 °2--1.33313792932 °2
S0.019708949919 Å °0.0235385778585 Å °-0.0730290676612 Å °0.245322128943 Å °0.0165349726094 Å °0.0341109936377 Å °-0.0707759799438 Å °0.0127845674472 Å °-0.0495341376371 Å °
Refinement TLS groupSelection details: all

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