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- PDB-4obf: Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Proteas... -

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Basic information

Entry
Database: PDB / ID: 4obf
TitleCrystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease Variant (D30N/N88D) in Complex with the p1-p6 substrate variant (S451N)
Components
  • HIV-1 Protease
  • p1-p6 peptide
KeywordsHYDROLASE / Co-evolution / Resistance
Function / homology
Function and homology information


viral budding via host ESCRT complex / 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 ...viral budding via host ESCRT complex / 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 / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / 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. ...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. / 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 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / 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
ACETATE ION / PHOSPHATE ION / Gag polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsKolli, M.
CitationJournal: J.Virol. / Year: 2014
Title: HIV-1 protease-substrate coevolution in nelfinavir resistance.
Authors: Kolli, M. / Ozen, A. / Kurt-Yilmaz, N. / Schiffer, C.A.
History
DepositionJan 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / 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: HIV-1 Protease
B: HIV-1 Protease
C: HIV-1 Protease
D: HIV-1 Protease
E: p1-p6 peptide
F: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,83622
Polymers45,6606
Non-polymers1,17616
Water3,387188
1
A: HIV-1 Protease
B: HIV-1 Protease
E: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,47912
Polymers22,8303
Non-polymers6499
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-18 kcal/mol
Surface area9390 Å2
MethodPISA
2
C: HIV-1 Protease
D: HIV-1 Protease
F: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,35710
Polymers22,8303
Non-polymers5277
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-24 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.547, 60.074, 60.232
Angle α, β, γ (deg.)90.00, 99.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDEF

#1: Protein
HIV-1 Protease / PR / Retropepsin


Mass: 10814.804 Da / Num. of mol.: 4 / Mutation: Q7K, D25N, D30N, V64I, N88D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: group M subtype B (isolate ARV2/SF2) / 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: 1200.350 Da / Num. of mol.: 2 / Fragment: UNP residues 446-455 / Mutation: S8N / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03349

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Non-polymers , 5 types, 204 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 32% Ammonium Sulphate, 63mM Sodium Citrate, 126mM 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: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2009 / Details: Mirrors
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 41265 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.066 / Net I/σ(I): 21.12
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.713 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.12 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.72 Å
Translation2.5 Å29.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.14data extraction
BioCARS-developedGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T3R

1t3r


Resolution: 1.68→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.485 / SU ML: 0.088 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22889 2076 5 %RANDOM
Rwork0.17974 ---
obs0.18217 39171 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.068 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å2-0.33 Å2
2--0.77 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.68→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 74 188 3345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223233
X-RAY DIFFRACTIONr_bond_other_d0.0010.022191
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9954386
X-RAY DIFFRACTIONr_angle_other_deg0.80635391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27525118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28115525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1961517
X-RAY DIFFRACTIONr_chiral_restr0.0970.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02563
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3671.52058
X-RAY DIFFRACTIONr_mcbond_other0.421.5861
X-RAY DIFFRACTIONr_mcangle_it2.22723326
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.25131175
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0254.51055
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 142 -
Rwork0.267 2782 -
obs--96.06 %
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)
14.04572.45553.31622.8466-0.08723.584-0.28970.35860.376-0.2390.03970.0439-0.21330.22140.250.157-0.01820.00670.13410.08970.1301-5.23513.892-12.4724
26.44263.0856-2.25691.9836-1.95762.2264-0.0169-0.26140.49010.0659-0.08730.0691-0.184-0.0230.10420.1285-0.0052-0.00710.0926-0.04220.1915-5.65296.61620.8749
39.9766-9.84161.951314.3183-3.44742.60560.08610.4961-0.7865-0.4852-0.1271-0.29450.0329-0.08020.0410.1588-0.02380.0370.1692-0.10660.1205-4.8765-9.2644-12.1686
44.87330.3623-1.24581.59940.68450.911-0.04310.20420.0439-0.04980.082-0.05560.0894-0.0368-0.03890.1231-0.0114-0.01380.09530.01350.0488-10.8449-5.5466-3.3238
55.9091-0.0735-0.33873.4222-0.1384-0.30960.0974-0.1926-0.25190.1528-0.02430.3326-0.0362-0.092-0.07310.1721-0.01790.00060.170.02550.1062-25.4001-11.36892.6569
64.0993-0.11250.30361.6934-0.27661.1348-0.0190.10050.2335-0.016-0.0171-0.0566-0.08660.0740.03610.11-0.01240.00350.07570.00290.06980.6007-2.7434-1.5105
77.322-0.811-0.24061.07880.87576.1002-0.0736-0.0265-0.1342-0.1303-0.0304-0.14130.00540.51010.1040.12960.00810.0060.10580.06570.126214.5415-7.93265.622
812.36454.2112-0.12443.32110.84411.3445-0.06110.2709-0.48380.05620.04990.2128-0.0840.05880.01120.14420.0019-0.00950.0818-0.00620.1758-12.4811-17.40243.1559
95.9814.33670.76462.67910.1051.2609-0.0086-0.45310.01690.0169-0.0286-0.01420.005-0.03160.03720.1467-0.0066-0.01350.2264-0.01320.09292.6288-7.067812.1907
1010.1837-6.04547.776612.4218-11.85214.04240.16610.3565-0.4589-0.260.08360.07370.3567-0.1217-0.24970.0794-0.0314-0.00780.063-0.03850.1316-24.2103-13.0552-2.9116
1110.53766.9972-2.90578.2445-1.29228.76070.1061-0.11590.6029-0.0465-0.03340.4971-0.34610.0286-0.07260.11110.00340.01010.11670.01260.1004-22.66961.1242-6.6121
123.23581.24580.28011.692-0.5535-0.2444-0.14730.4291-0.0869-0.18920.1502-0.05790.0613-0.0295-0.00290.1593-0.03230.02570.19330.01070.0443-21.9043-4.174-8.3958
133.52312.9338-5.15419.4444-13.854220.06040.1146-0.24630.12160.3357-0.3477-0.2513-0.23960.53510.23320.122-0.0387-0.03450.1212-0.00460.116113.8155-1.66.7974
1417.6971-0.7176-2.07035.34560.15937.07880.10380.7687-0.0508-0.4032-0.0220.0266-0.2691-0.1392-0.08180.1264-0.00640.00970.05440.03280.110712.4026-0.3356-8.2273
155.63814.3195-3.6913.7671-1.00746.64710.01780.15650.3892-0.12670.00270.1188-0.3175-0.2174-0.02050.11710.0365-0.02510.07490.05890.197110.76361.9441-2.1871
166.59530.3076-1.2489-0.08361.75942.76410.1922-0.1691-0.14980.10850.0928-0.0995-0.0810.1396-0.28510.18560.0084-0.00450.10240.00330.107-14.6325-6.37984.4812
172.1194-1.13840.59272.79650.7120.72880.06130.1098-0.1309-0.0419-0.147-0.05370.09260.09640.08570.1564-0.00670.02060.10760.00960.12024.2677-10.04811.0127
187.9584-0.82032.94020.6037-1.2342.2245-0.10830.2555-0.0009-0.04150.0213-0.05850.0294-0.0180.0870.157-0.003-0.0080.16940.01160.0571-13.7553-4.8177-10.463
1910.36990.6261-1.20536.4891-1.17121.0458-0.02480.01190.31790.0279-0.0682-0.270.08020.10110.0930.1027-0.01210.00750.04440.01520.14923.22994.3591-3.0735
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1B1 - 5
4X-RAY DIFFRACTION1B94 - 99
5X-RAY DIFFRACTION2A6 - 10
6X-RAY DIFFRACTION3B6 - 10
7X-RAY DIFFRACTION4A22 - 32
8X-RAY DIFFRACTION5A33 - 43
9X-RAY DIFFRACTION6B22 - 32
10X-RAY DIFFRACTION7B33 - 43
11X-RAY DIFFRACTION8A44 - 49
12X-RAY DIFFRACTION8A52 - 56
13X-RAY DIFFRACTION9B44 - 49
14X-RAY DIFFRACTION9B52 - 56
15X-RAY DIFFRACTION10A57 - 62
16X-RAY DIFFRACTION11A63 - 68
17X-RAY DIFFRACTION12A69 - 76
18X-RAY DIFFRACTION13B57 - 62
19X-RAY DIFFRACTION14B63 - 68
20X-RAY DIFFRACTION15B69 - 76
21X-RAY DIFFRACTION16A77 - 85
22X-RAY DIFFRACTION17B77 - 85
23X-RAY DIFFRACTION18A86 - 93
24X-RAY DIFFRACTION19B86 - 93

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