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- PDB-7n6t: Crystal structure of inhibitor-free HIV-1 PRS17 revertant mutant ... -

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Basic information

Entry
Database: PDB / ID: 7n6t
TitleCrystal structure of inhibitor-free HIV-1 PRS17 revertant mutant PRS17 V48G
ComponentsProtease
KeywordsHYDROLASE / HIV-1 Protease / drug resistance / PRS17
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å
AuthorsBurnaman, S.H. / Wang, Y.-F. / Weber, I.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150461 United States
CitationJournal: J.Mol.Graph.Model. / Year: 2021
Title: Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17.
Authors: Burnaman, S.H. / Kneller, D.W. / Wang, Y.F. / Kovalevsky, A. / Weber, I.T.
History
DepositionJun 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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:
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Assembly

Deposited unit
A: Protease
B: Protease


Theoretical massNumber of molelcules
Total (without water)21,5012
Polymers21,5012
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-17 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.340, 45.340, 105.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Protease / PR / Retropepsin


Mass: 10750.565 Da / Num. of mol.: 2
Mutation: Q7K, L10I, K20R, L33I, E35D, M36I, S37D, M46L, I54V, D60E, I62V, L63P, C67A, A71V, I72V, V77I, V82S, L90M, I93L, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)
Strain: isolate BRU/LAI / Gene: gag-pol / Variant: PRS17 V48G / Plasmid: pJ414 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5, 20% w/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 48738 / % possible obs: 97.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.029 / Rrim(I) all: 0.064 / Χ2: 1.043 / Net I/σ(I): 15.5 / Num. measured all: 228228
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.32-1.373.30.52843120.8770.3060.6141.01486.1
1.37-1.424.20.44549530.9480.2380.5061.06299.6
1.42-1.494.70.34949360.9660.1830.3951.081100
1.49-1.574.70.24349900.9760.1280.2751.07499.5
1.57-1.664.60.1747800.9810.090.1931.06396.5
1.66-1.795.10.12249830.9880.0620.1371.00599.7
1.79-1.974.80.08849620.9920.0460.11.02999.2
1.97-2.264.60.06748250.9940.0360.0761.04896.9
2.26-2.845.30.05349790.9940.0270.0591.04699.3
2.84-505.20.0550180.9950.0250.0561.00699.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.88 Å32.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PHASER2.8.3phasing
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z4x

4z4x


Resolution: 1.32→34.35 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.217 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2486 5.1 %RANDOM
Rwork0.1577 ---
obs0.1592 46202 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.95 Å2 / Biso mean: 23.991 Å2 / Biso min: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2---1.19 Å2-0 Å2
3---2.38 Å2
Refinement stepCycle: final / Resolution: 1.32→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 0 161 1677
Biso mean---29.88 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131617
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171684
X-RAY DIFFRACTIONr_angle_refined_deg2.1941.652216
X-RAY DIFFRACTIONr_angle_other_deg1.5871.5783884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80821.66772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84615294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8781512
X-RAY DIFFRACTIONr_chiral_restr0.1190.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021815
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02345
X-RAY DIFFRACTIONr_rigid_bond_restr11.50733301
LS refinement shellResolution: 1.32→1.352 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.277 132 -
Rwork0.26 2846 -
obs--80.33 %

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