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- PDB-3lzs: Crystal Structure of HIV-1 CRF01_AE Protease in Complex with Darunavir -

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Basic information

Entry
Database: PDB / ID: 3lzs
TitleCrystal Structure of HIV-1 CRF01_AE Protease in Complex with Darunavir
ComponentsHIV-1 protease
KeywordsHYDROLASE / HIV-1 protease / non-B clades / CRF01_AE / inhibitor resistance / AIDS / Aspartyl protease
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 / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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-017 / ACETATE ION / Gag-Pol polyprotein / HIV-1 protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSchiffer, C.A. / Bandaranayake, R.M.
CitationJournal: J.Virol. / Year: 2010
Title: The Effect of Clade-Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways.
Authors: Bandaranayake, R.M. / Kolli, M. / King, N.M. / Nalivaika, E.A. / Heroux, A. / Kakizawa, J. / Sugiura, W. / Schiffer, C.A.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.4Sep 6, 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

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)22,2586
Polymers21,5342
Non-polymers7254
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-26 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.164, 62.164, 82.705
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HIV-1 protease


Mass: 10766.799 Da / Num. of mol.: 2 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NH1 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106
References: UniProt: Q9QB59, UniProt: P24740*PLUS, HIV-1 retropepsin
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. obs: 12493 / % possible obs: 93.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.066 / Χ2: 0.973 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.027.50.36313430.762100
2.02-2.17.40.25613070.785100
2.1-2.27.40.19813240.878100
2.2-2.316.60.2437471.07956.8
2.31-2.467.40.13513311.057100
2.46-2.657.30.10113161.062100
2.65-2.917.30.0813301.0899.9
2.91-3.337.10.06613321.07499.9
3.33-4.26.40.05711050.99183
4.2-1006.80.0413581.03398.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TSU

1tsu


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.781 / SU B: 8.909 / SU ML: 0.146 / SU R Cruickshank DPI: 0.222 / SU Rfree: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 611 4.9 %RANDOM
Rwork0.2 ---
obs0.203 12399 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.07 Å2 / Biso mean: 19.149 Å2 / Biso min: 5.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 50 69 1565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221561
X-RAY DIFFRACTIONr_bond_other_d0.0010.021024
X-RAY DIFFRACTIONr_angle_refined_deg1.5482.0522130
X-RAY DIFFRACTIONr_angle_other_deg0.85232526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10425.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48715240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.001156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_mcbond_it0.8771.5985
X-RAY DIFFRACTIONr_mcbond_other0.2181.5414
X-RAY DIFFRACTIONr_mcangle_it1.51421575
X-RAY DIFFRACTIONr_scbond_it2.0043576
X-RAY DIFFRACTIONr_scangle_it3.1264.5555
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 53 -
Rwork0.237 930 -
all-983 -
obs--99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.81720.0875-2.03134.6925-5.37256.93880.19780.20250.42370.23050.17810.1805-0.3584-0.3524-0.37590.18530.00390.0140.2273-0.02880.1111-19.813530.71790.9109
24.03390.4153-5.81995.6743.080910.81720.20680.04760.285-0.1022-0.00860.3375-0.4385-0.0517-0.19810.1365-0.0031-0.03390.15750.04380.1188-16.728832.2417-0.923
34.8554-1.81270.99985.7233.27237.06120.1083-0.2323-0.33280.34330.0006-0.0450.646-0.1974-0.10890.0941-0.05880.03140.20140.01320.1062-21.317320.4566.177
49.6942-2.83869.61344.457-3.293218.63780.2730.3948-0.3235-0.2142-0.06680.08590.47650.7265-0.20620.1391-0.07630.02080.12920.01450.0858-7.240128.388-6.2601
51.7951.04161.53011.81450.4041.5264-0.01630.059-0.0589-0.0699-0.0094-0.1767-0.04220.05350.02570.1086-0.02620.0050.1581-0.01960.1061-13.807119.3645-5.2862
66.0384-1.97660.2260.82820.82028.3810.00040.2661-0.6610.1034-0.05680.2290.8059-0.60380.05630.1907-0.0374-0.00650.2019-0.10370.2014-17.33037.2908-15.8877
72.62760.12781.73791.21171.10652.151-0.0464-0.0391-0.1455-0.0020.04380.06350.0401-0.12510.00260.0991-0.0639-0.00510.15560.00790.1049-9.706621.78415.2044
81.18031.69260.76598.4992-0.6558.36890.2792-0.0415-0.20430.557-0.3227-0.7902-0.0671.55670.04350.0939-0.0617-0.09650.32210.04210.1412.286818.879215.6359
97.5535-2.76662.11922.3585-0.316420.67330.47640.9992-0.0141-0.2049-0.40870.15490.54010.6979-0.06770.07250.04780.01320.21870.05860.1506-4.809510.4461-11.5002
103.87044.66461.59918.00946.36478.9242-0.22230.1441-0.8263-0.00340.1718-0.7530.32790.19880.05040.18850.0508-0.03820.2004-0.07780.2613-4.87837.2139-7.5054
113.5412-1.1997-2.2486.40571.530325.46990.2122-0.4828-0.37161.26720.10160.22370.48680.2613-0.31380.3284-0.05510.02060.09820.00040.1757-6.39869.434811.7388
121.38912.75682.17587.5524-0.830216.24950.1363-0.2107-0.13940.1378-0.2713-0.37120.3399-0.67460.1350.12950.0279-0.09230.0962-0.03250.1447-4.54218.2137.4165
132.4558-5.77133.818916.5031-4.520113.14880.49620.3545-0.274-1.1063-0.33780.68610.70710.7613-0.15830.0880.038-0.04310.6375-0.2110.0928-14.134811.328-18.611
147.08693.9479-2.1382.3478-3.460535.3860.3441-0.43980.63710.2572-0.20580.3563-1.185-0.4526-0.13820.1558-0.0582-0.02710.1443-0.02330.1812-25.9920.4267-13.0921
158.6535-7.21672.30627.8501-2.21065.7814-0.14480.4927-0.1824-0.17430.11320.2429-0.09670.11670.03170.0526-0.0945-0.0120.17990.00620.0686-19.527619.8343-16.0673
1610.9857-7.8843-1.8038.97011.53264.3177-0.1828-0.6984-0.07371.26510.2961-0.29370.56210.2637-0.11320.4404-0.0479-0.13120.1140.03990.0457-2.692717.879518.573
176.12244.8563-7.32564.8872-0.558235.4339-0.030.25860.5314-0.17810.09790.5301-0.8441-0.7566-0.06790.0515-0.0257-0.0220.1395-0.01420.162-4.738132.603512.9727
182.76380.9387-1.87188.84363.18196.64050.2402-0.39510.03450.4255-0.21960.25280.1399-0.1654-0.02070.0474-0.0549-0.00930.1409-0.01680.072-7.360226.878515.9935
198.0228-8.2345-1.742611.01851.46338.2956-0.2614-0.0363-0.28720.7287-0.0047-0.27350.57680.16120.26620.1791-0.0624-0.06560.0996-0.0110.1445-15.155410.6759-5.3716
201.9589-0.38242.845613.843-3.32344.70150.2810.3372-0.0226-0.1959-0.3202-0.12220.44290.51620.03930.0666-0.00960.02850.2022-0.05340.1837-1.68518.44925.3761
214.8182-0.04893.96674.880.05325.2885-0.06050.10650.053-0.42840.1660.1701-0.22260.0181-0.10550.1068-0.0548-0.00220.15590.01690.0841-15.445924.9476-10.5414
226.2329-2.55770.97376.13065.65767.6819-0.0876-0.39160.3367-0.09180.0718-0.1793-0.1361-0.30650.01590.0831-0.05610.0120.1718-0.00510.062-13.857225.755710.4317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION2B1 - 5
4X-RAY DIFFRACTION2B94 - 99
5X-RAY DIFFRACTION3A6 - 10
6X-RAY DIFFRACTION4B6 - 10
7X-RAY DIFFRACTION5A22 - 32
8X-RAY DIFFRACTION6A33 - 43
9X-RAY DIFFRACTION7B22 - 32
10X-RAY DIFFRACTION8B33 - 43
11X-RAY DIFFRACTION9A44 - 49
12X-RAY DIFFRACTION10A52 - 56
13X-RAY DIFFRACTION11B44 - 49
14X-RAY DIFFRACTION12B52 - 56
15X-RAY DIFFRACTION13A57 - 62
16X-RAY DIFFRACTION14A63 - 68
17X-RAY DIFFRACTION15A69 - 76
18X-RAY DIFFRACTION16B57 - 62
19X-RAY DIFFRACTION17B63 - 68
20X-RAY DIFFRACTION18B69 - 76
21X-RAY DIFFRACTION19A77 - 85
22X-RAY DIFFRACTION20B77 - 85
23X-RAY DIFFRACTION21A86 - 93
24X-RAY DIFFRACTION22B86 - 93

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