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- PDB-4qj7: Crystal structure of inactive HIV-1 protease variant (I50V/A71V) ... -

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Basic information

Entry
Database: PDB / ID: 4qj7
TitleCrystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with p1-p6 substrate variant (R452S)
Components
  • Protease
  • p1-p6 peptide
KeywordsHYDROLASE / co-evolution / protease
Function / homology
Function and homology information


viral budding via host ESCRT complex / RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / RNA stem-loop binding / host cell / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal 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 ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Gag polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsLin, K.H. / Schiffer, C.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.
Authors: Ozen, A. / Lin, K.H. / Kurt Yilmaz, N. / Schiffer, C.A.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
C: Protease
D: Protease
F: p1-p6 peptide
G: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8099
Polymers45,5226
Non-polymers2873
Water5,891327
1
A: Protease
B: Protease
F: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9525
Polymers22,7613
Non-polymers1912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-43 kcal/mol
Surface area9450 Å2
MethodPISA
2
C: Protease
D: Protease
G: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8574
Polymers22,7613
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-44 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.597, 58.162, 61.758
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protease / / Retropepsin


Mass: 10828.831 Da / Num. of mol.: 4 / Mutation: Q7K, N25D, D25N, I50V, A71V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (ARV2/SF2 ISOLATE)
Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide p1-p6 peptide


Mass: 1103.209 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 (ARV2/SF2 ISOLATE)
References: UniProt: P03349*PLUS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: ammonium sulfate, sodium citrate, sodium phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2011
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 115828 / Num. obs: 40242 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.047 / Net I/σ(I): 20.77
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 5.86 / Num. unique all: 4101 / Rsym value: 0.19 / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→41.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.186 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22926 2045 5.1 %RANDOM
Rwork0.17845 ---
obs0.18102 38190 94.47 %-
all-115828 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0 Å2-0.24 Å2
2--0.06 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.67→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 15 327 3480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193404
X-RAY DIFFRACTIONr_bond_other_d0.0010.023434
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9884655
X-RAY DIFFRACTIONr_angle_other_deg0.72237916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59225.372121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39215597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.761515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
X-RAY DIFFRACTIONr_mcbond_it1.4122.1351762
X-RAY DIFFRACTIONr_mcbond_other1.412.1351761
X-RAY DIFFRACTIONr_mcangle_it2.3143.1952227
X-RAY DIFFRACTIONr_mcangle_other2.3143.1962228
X-RAY DIFFRACTIONr_scbond_it1.7982.4271642
X-RAY DIFFRACTIONr_scbond_other1.7562.4131631
X-RAY DIFFRACTIONr_scangle_other2.7983.5212411
X-RAY DIFFRACTIONr_long_range_B_refined5.12818.3173664
X-RAY DIFFRACTIONr_long_range_B_other5.12818.323665
LS refinement shellResolution: 1.667→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 155 -
Rwork0.234 2802 -
obs-4101 94.78 %

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