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- PDB-4jec: Joint neutron and X-ray structure of per-deuterated HIV-1 proteas... -

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Basic information

Entry
Database: PDB / ID: 4jec
TitleJoint neutron and X-ray structure of per-deuterated HIV-1 protease in complex with clinical inhibitor amprenavir
ComponentsHIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / hydrolysis / polypeptides / HYDROLASE-HYDROLASE INHIBITOR complex
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 / 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
Chem-478 / DEUTERATED WATER / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKovalevsky, A.Y. / Weber, I.T. / Langan, P.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Joint X-ray/Neutron Crystallographic Study of HIV-1 Protease with Clinical Inhibitor Amprenavir: Insights for Drug Design.
Authors: Weber, I.T. / Waltman, M.J. / Mustyakimov, M. / Blakeley, M.P. / Keen, D.A. / Ghosh, A.K. / Langan, P. / Kovalevsky, A.Y.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Refinement description
Category: diffrn_detector / diffrn_radiation ...diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / refine
Item: _diffrn_detector.details / _diffrn_detector.pdbx_collection_date ..._diffrn_detector.details / _diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_all / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_diffrn_id / _refine.pdbx_ls_sigma_F / _refine.pdbx_refine_id
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / 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 / _refine_hist.d_res_high / _refine_hist.d_res_low / _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: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0224
Polymers21,4812
Non-polymers5412
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint0 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.186, 87.431, 46.405
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 / Protease / PR / Retropepsin


Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-478 / {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER / Amprenavir


Mass: 505.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N3O6S / Comment: protease inhibitor, medication*YM
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 131 / 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
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, pH=6; 0.8M NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODEIN-HOUSERIGAKU MICROMAX-007 HF11.541.54
NUCLEAR REACTORLADI-IIIOTHER22.8-4.02.8-4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATENov 1, 2012RIGAKU OSMIC VariMax
MAATEL CYLINDRICAL2IMAGE PLATEOct 2, 2012SET OF COLLIMATORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
341
Reflection

Entry-ID: 4JEC

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-59.111280050.93.20.12817.5
2-401600694.97.10.074236.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.113.10.2694.1164.9
2-2.076.60.4944.9285

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Processing

Software
NameVersionClassificationNB
nCNS1.0.0refinement
MAATELdata collection
LAUEGENdata reduction
LSCALEdata scaling
CNSphasing
Refinement

Biso max: 85.59 Å2 / Biso mean: 30.53 Å2 / Biso min: 10.58 Å2 / Rfactor Rfree error: 0.008 / R Free selection details: random / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used / Bsol: 49.6308 Å2 / ksol: 0.291021 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDRfactor obsσ(F)
2.01-19.77X-RAY DIFFRACTION0.2030.19472416681147194.988.21
2-20NEUTRON DIFFRACTION0.2610.24456512800577.320.2443
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Luzzati d res high-2.01
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
X-RAY DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.01→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 36 131 1679
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.008
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_torsion_deg17.2
NEUTRON DIFFRACTIONx_torsion_impr_deg0.88
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg17.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.88
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 (%)
2-2.090.4474250.4271009NEUTRON DIFFRACTION0.0692056150750.9
2.1-2.210.218955.70.2141569NEUTRON DIFFRACTION0.0222050166481.2
2.21-2.350.279945.30.2251667NEUTRON DIFFRACTION0.0292055176185.7
2.35-2.530.207854.80.2171688NEUTRON DIFFRACTION0.0222033177387.2
2.53-2.780.196854.50.2091800NEUTRON DIFFRACTION0.0212085188590.4
2.78-3.180.239934.80.2061843NEUTRON DIFFRACTION0.0252080193693.1
3.18-40.18610150.181919NEUTRON DIFFRACTION0.0192110202095.7
4-19.770.1771034.70.1722070NEUTRON DIFFRACTION0.0172223217397.8
2-2.090.4474240.4271009X-RAY DIFFRACTION0.0692062105150.9
2.09-2.20.349534.60.3721107X-RAY DIFFRACTION0.0482097116055.3
2.2-2.340.3486250.3461190X-RAY DIFFRACTION0.0442057125260.9
2.34-2.520.305695.30.2991245X-RAY DIFFRACTION0.0372077131463.3
2.52-2.770.288654.50.2621379X-RAY DIFFRACTION0.0362097144468.9
2.77-3.170.2417950.2211515X-RAY DIFFRACTION0.0272102159475.8
3.17-3.990.208965.10.1851788X-RAY DIFFRACTION0.0212142188487.9
3.99-19.370.205994.70.1791995X-RAY DIFFRACTION0.0212237209493.6

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