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- PDB-5e5k: Joint X-ray/neutron structure of HIV-1 protease triple mutant (V3... -

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Basic information

Entry
Database: PDB / ID: 5e5k
TitleJoint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 4.3
ComponentsHIV-1 protease
KeywordsHydrolase/hydrolase inhibitor / protease drug resistant mutant inhibitor complex / Hydrolase-hydrolase 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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-017 / DEUTERATED WATER / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKovalevsky, A.Y. / Das, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.
Authors: Gerlits, O. / Wymore, T. / Das, A. / Shen, C.H. / Parks, J.M. / Smith, J.C. / Weiss, K.L. / Keen, D.A. / Blakeley, M.P. / Louis, J.M. / Langan, P. / Weber, I.T. / Kovalevsky, A.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_radiation ...citation / diffrn_radiation / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_radiation.pdbx_diffrn_protocol / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0573
Polymers21,5092
Non-polymers5481
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-0 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.593, 87.428, 46.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HIV-1 protease / Pr160Gag-Pol


Mass: 10754.703 Da / Num. of mol.: 2 / Mutation: Q7K, V32I, L33I, I47V, L63I, C67A, V82I, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate BRU/LAI / Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03367, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03367, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: NaCl, MES / PH range: 4.3

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D22.8-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATENov 8, 2014OSMIC VARIMAX
MAATEL IMAGINE2IMAGE PLATEDec 4, 2014ELLIPTICAL MIRRORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
341
ReflectionResolution: 1.75→40 Å / Num. obs: 21726 / % possible obs: 86.2 % / Redundancy: 4.3 % / Net I/σ(I): 34

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
nCNS1.0.0refinement
LAUEGENdata reduction
LSCALEdata scaling
Refinement

Biso max: 92.87 Å2 / Biso mean: 27.64 Å2 / Biso min: 8.91 Å2 / Diffraction-ID: 1 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 4JEC

4jec

/ Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)Bsol (Å2)ksol (e/Å3)
1.75-33.74X-RAY DIFFRACTION0.2180.0070.2039491825225099192014.976.546.03580.287805
2.3-36.58NEUTRON DIFFRACTION0.2240.0120.21233775111124978484.369.848.39370.524466
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.210.2
Luzzati d res low-5
Luzzati sigma a0.140.13
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.290.28
Luzzati d res low-5
Luzzati sigma a0.560.52
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJoint X-ray/neutron ML
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 1.75→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 38 105 1657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg18.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.96
NEUTRON DIFFRACTIONx_bond_d0.009
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg18.9
NEUTRON DIFFRACTIONx_torsion_impr_deg0.96
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.75-1.830.227785.60.2511314X-RAY DIFFRACTION0.0263083139245.1
1.83-1.930.2321175.30.232102X-RAY DIFFRACTION0.0213101221971.5
1.93-2.050.2531094.40.2082351X-RAY DIFFRACTION0.0243084246079.8
2.05-2.20.251325.10.2132462X-RAY DIFFRACTION0.0223126259483
2.2-2.430.2313050.2162483X-RAY DIFFRACTION0.023096261384.4
2.43-2.780.22913250.2222514X-RAY DIFFRACTION0.023134264684.4
2.78-3.50.2081254.70.2092530X-RAY DIFFRACTION0.0193176265583.6
3.5-33.740.1991264.80.1782496X-RAY DIFFRACTION0.0183324262278.9
2.3-2.40.3994260.347656NEUTRON DIFFRACTION0.062136069851.3
2.4-2.530.358374.80.343735NEUTRON DIFFRACTION0.059137277256.3
2.53-2.690.306374.60.289771NEUTRON DIFFRACTION0.05139980857.8
2.69-2.90.246283.20.251835NEUTRON DIFFRACTION0.046138886362.1
2.9-3.190.1623940.172947NEUTRON DIFFRACTION0.026138498671.2
3.19-3.650.181554.90.1811071NEUTRON DIFFRACTION0.0241413112679.6
3.65-4.60.172534.10.1451227NEUTRON DIFFRACTION0.0241433128089.3
4.6-36.580.155463.50.1871269NEUTRON DIFFRACTION0.0231506131587.3

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