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- PDB-4qlh: Crystal structure of drug resistant V82S/V1082S HIV-1 Protease -

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Basic information

Entry
Database: PDB / ID: 4qlh
TitleCrystal structure of drug resistant V82S/V1082S HIV-1 Protease
ComponentsProtease, linker, Protease
KeywordsHYDROLASE / Tethered HIV-1 Protease dimer / Peptide bond hydrolysis
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / identical protein 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
synthetic (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDas, A. / Raskar, T. / Hosur, M.V.
CitationJournal: To be Published
Title: Crystal structure of drug resistant V82S/V1082S HIV-1 Protease
Authors: Hosur, M.V.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Other
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_ec ..._entity.details / _entity.pdbx_ec / _entity.pdbx_fragment / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.3Nov 8, 2023Group: 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: Protease, linker, Protease


Theoretical massNumber of molelcules
Total (without water)21,8191
Polymers21,8191
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.490, 62.490, 83.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease, linker, Protease


Mass: 21818.537 Da / Num. of mol.: 1 / Fragment: UNP residues 489-587,UNP residues 489-587 / Mutation: V82S, V1082S, M95A, M1095A
Source method: isolated from a genetically manipulated source
Details: Protease-linker-Protease
Source: (gene. exp.) Human immunodeficiency virus 1, (gene. exp.) synthetic (others)
Gene: pol / Production host: Escherichia coli (E. coli)
References: UniProt: Q72874, UniProt: P04585*PLUS, HIV-1 retropepsin, HIV-1 retropepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Protein concentration - 2.2 mg/ml in Sodium Acetate buffer - 50mM Sodium Acetate and 0.1% Beta Mercaptoethanol pH 4.5 Precipitant - 0.9% Ammonium Sulphate in Phosphate Citrate buffer - 0.2M ...Details: Protein concentration - 2.2 mg/ml in Sodium Acetate buffer - 50mM Sodium Acetate and 0.1% Beta Mercaptoethanol pH 4.5 Precipitant - 0.9% Ammonium Sulphate in Phosphate Citrate buffer - 0.2M Sodium dihydrogen phosphate and 0.1M Trisodium Citrate pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2012
RadiationMonochromator: Helios optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→33.04 Å / Num. all: 6924 / Num. obs: 6182 / % possible obs: 89.2 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.44-2.57150.9
2.57-2.73195.5
2.73-2.92195.7
2.92-3.15195.7
3.15-3.45195.2
3.45-33.04195.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LV1

1lv1


Resolution: 2.45→31.25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.896 / SU B: 21.077 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 3 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25597 274 4.7 %RANDOM
Rwork0.19216 ---
obs0.1953 5260 89.46 %-
all-5880 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.839 Å2
Refinement stepCycle: LAST / Resolution: 2.45→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 0 58 1566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191534
X-RAY DIFFRACTIONr_bond_other_d0.0050.021578
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9852078
X-RAY DIFFRACTIONr_angle_other_deg0.78933630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0165196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89224.81554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30715280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.574158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02314
LS refinement shellResolution: 2.446→2.509 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 9 -
Rwork0.272 143 -
all-152 -
obs--29.46 %
Refinement TLS params.Method: refined / Origin x: 23.2626 Å / Origin y: 0.0092 Å / Origin z: 0.0641 Å
111213212223313233
T0.0731 Å20.003 Å20.0013 Å2-0.0725 Å20.0008 Å2--0.0594 Å2
L0.1724 °20.0072 °2-0.0074 °2-0.4132 °2-0.2524 °2--0.1627 °2
S0.0067 Å °-0.0011 Å °-0.0057 Å °0.0136 Å °0.028 Å °0.0229 Å °-0.0158 Å °-0.0082 Å °-0.0347 Å °

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