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- PDB-8dci: Crystal Structure of a highly resistant HIV-1 protease Clinical i... -

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Basic information

Entry
Database: PDB / ID: 8dci
TitleCrystal Structure of a highly resistant HIV-1 protease Clinical isolate PR10x (inhibitor-free)
ComponentsProtease
KeywordsVIRAL PROTEIN / HYDROLASE / HIV/AIDS / HIV protease / drug resistant clinical mutant / evolution of drug resistance / distal mutations
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsWong-Sam, A.E. / Wang, Y.-F. / Weber, I.T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)AI150461 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)AI150466 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)an NIH diversity supplement United States
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: J.Mol.Graph.Model. / Year: 2022
Title: HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics.
Authors: Wong-Sam, A. / Wang, Y.F. / Kneller, D.W. / Kovalevsky, A.Y. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T.
History
DepositionJun 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease


Theoretical massNumber of molelcules
Total (without water)21,5692
Polymers21,5692
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-14 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.366, 81.351, 85.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease / / PR / Retropepsin


Mass: 10784.560 Da / Num. of mol.: 2
Mutation: Q7K, L10F, I13V, L19I, K20T, V32I, L33I, E35N, M36I, M46I, G48Q, I54L, L63P, C67E, A71V, T74S, L76V, I84V, L89V, L90M, T91S, I93L, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: Clinical isolate PR10x / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03367, HIV-1 retropepsin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Hanging-drop vapor diffusion using equal volumes of protein stock (3.9 mg/mL) and well reservoir solution. Cryoprotected in 30% glycerol. Crystallized in 0.85 M NaCl and 0.1 M sodium acetate pH 5.4

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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: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 25357 / % possible obs: 97.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Χ2: 1 / Net I/σ(I): 16.5 / Num. measured all: 148165
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.685.30.47624170.8950.2240.5281.00195
1.68-1.7560.38224930.940.1690.4191.00398.8
1.75-1.826.40.26725010.9720.1160.2921.00299
1.82-1.926.20.225460.980.0880.2191.00199.2
1.92-2.0460.15425590.9850.0690.1690.99899.3
2.04-2.25.80.12325270.9860.0560.136198.6
2.2-2.425.40.09924110.9890.0470.110.99394.2
2.42-2.776.30.08325820.9930.0370.0910.99699
2.77-3.495.80.06426160.9950.0290.070.99999.3
3.49-505.30.05427050.9960.0250.0591.00496.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.62 Å29.49 Å
Translation1.62 Å29.49 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L3S

7l3s
PDB Unreleased entry


Resolution: 1.62→29.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2621 / WRfactor Rwork: 0.2317 / FOM work R set: 0.8593 / SU B: 1.841 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0973 / SU Rfree: 0.0993 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1232 4.9 %RANDOM
Rwork0.1887 ---
obs0.1904 24067 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.06 Å2 / Biso mean: 26 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.62→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 0 126 1648
Biso mean---29.88 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131579
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171614
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.6422154
X-RAY DIFFRACTIONr_angle_other_deg1.3491.5753722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6995206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85423.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30515282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.345158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
LS refinement shellResolution: 1.622→1.664 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 73 -
Rwork0.253 1635 -
all-1708 -
obs--89.66 %

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