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

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Basic information

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


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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
PHOSPHATE ION / Gag polyprotein / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 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)46,59919
Polymers45,6066
Non-polymers99313
Water3,603200
1
A: HIV-1 Protease
B: HIV-1 Protease
E: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2689
Polymers22,8033
Non-polymers4656
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-26 kcal/mol
Surface area9510 Å2
MethodPISA
2
C: HIV-1 Protease
D: HIV-1 Protease
F: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,33010
Polymers22,8033
Non-polymers5277
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-24 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.672, 60.114, 60.196
Angle α, β, γ (deg.)90.00, 99.09, 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, 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: 1173.325 Da / Num. of mol.: 2 / Fragment: UNP residues 446-455 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03349, UniProt: P04591*PLUS

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Non-polymers , 4 types, 213 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 39.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 5000, 0.1M ammonium sulfate, 0.5M MES monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.033 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2009 / Details: Mirrors
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 34288 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.068 / Net I/σ(I): 14.7
Reflection shellResolution: 1.78→1.86 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.88 / Rsym value: 0.355 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.01 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.9 Å
Translation2.5 Å38.9 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: 1.78→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 4.999 / SU ML: 0.121 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25461 1711 5 %RANDOM
Rwork0.20039 ---
obs0.20312 32455 97.75 %-
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: 29.977 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å2-0.48 Å2
2--0.83 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 62 200 3322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223196
X-RAY DIFFRACTIONr_bond_other_d00.022142
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9964347
X-RAY DIFFRACTIONr_angle_other_deg0.78335285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4495419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.16224.953107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52815510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9421515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
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_it1.3351.52065
X-RAY DIFFRACTIONr_mcbond_other0.4111.5864
X-RAY DIFFRACTIONr_mcangle_it2.18423337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.23531131
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0484.51005
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: 1.78→1.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 102 -
Rwork0.216 2047 -
obs--83.65 %
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)
10.69050.88162.37691.70850.94713.285-0.09690.10960.1922-0.1528-0.02330.0589-0.1780.12670.12020.0867-0.01910.00850.07020.05330.0853-5.82163.859-12.3759
27.87352.0366-1.17380.8318-1.25893.0599-0.0172-0.1660.4172-0.0060.02690.17260.13080.0635-0.00970.06620.0044-0.00660.001-0.03070.1068-5.6576.61090.8776
35.8706-1.53020.37187.6765-3.11182.88350.09860.3069-0.1557-0.2154-0.01240.28820.21970.034-0.08620.07320.00130.02430.0818-0.03650.0247-4.8326-9.0774-12.302
43.8384-0.5116-0.87671.76511.07912.3682-0.06150.15080.0089-0.11870.05020.04220.08990.02110.01130.0596-0.0107-0.01490.01170.00360.023-10.9333-5.6281-3.3344
56.1116-0.4619-0.07253.134-0.2147-0.19220.0312-0.1949-0.07690.0559-0.01760.0939-0.0318-0.0908-0.01370.0853-0.01250.0130.08260.01380.0071-25.2326-10.87153.1369
63.0689-1.6614-0.34521.0818-0.056-0.2570.01130.04060.05230.0062-0.077-0.0664-0.12660.04610.06570.0846-0.0124-0.01850.03730.01290.04680.5875-2.7766-1.4289
75.1294-0.19521.3331-0.29070.55812.94480.02690.0803-0.07880.03520.0062-0.05320.10020.2328-0.03310.0939-0.0042-0.01110.03990.04250.080914.589-7.79445.7625
89.553.47330.40014.37350.1548-0.0841-0.01580.2513-0.35320.17160.06250.1321-0.07350.08-0.04670.0774-0.01490.00410.0176-0.01350.0688-12.3851-17.35923.363
96.2652.42071.58340.60510.46370.4650.0121-0.3923-0.03410.0114-0.0090.01130.0834-0.0478-0.00310.08940.0074-0.01380.10790.00760.04672.5743-7.063612.19
105.7575-2.50464.3133.3265-5.724810.6580.06190.1126-0.2942-0.00690.18580.04180.0904-0.2271-0.24770.0428-0.01120.00390.0267-0.03330.064-24.0429-13.0544-1.8891
114.53882.0937-1.11671.51660.94693.6682-0.0381-0.06480.1322-0.1565-0.0312-0.0194-0.22180.09270.06930.085100.0130.07750.01750.0882-22.88021.2472-6.7908
121.8698-0.1721.4942-0.52430.86791.23-0.02330.212-0.1518-0.173-0.0111-0.1440.10180.01330.03430.0991-0.03750.03140.1078-0.00180.0187-21.3199-5.2029-8.008
132.98532.2662-3.0835.3871-6.45169.08350.1754-0.15870.09070.1752-0.1957-0.2177-0.0220.38420.02030.0437-0.0152-0.01780.0489-0.01020.04813.9115-1.4796.7209
1421.8920.7545.34483.289-0.00717.2119-0.03120.5369-0.2459-0.22220.26570.233-0.36330.2193-0.23460.095-0.0079-0.01370.01190.02060.042212.4673-0.3398-8.1916
152.21021.9306-2.28583.2812-0.67473.70880.0210.04290.2991-0.08140.05090.0677-0.1966-0.2061-0.07190.06210.0096-0.03120.03090.01710.108410.76031.9099-2.2341
164.64420.52330.17980.55770.4355-0.23480.0506-0.16440.00780.16320.04850.0317-0.0046-0.0415-0.09910.10050.00590.01340.0292-0.00290.0522-14.6831-6.39674.57
171.3057-0.28-0.38423.34381.93291.13730.05550.132-0.08660.0589-0.17490.18750.11180.05320.11940.08880.01530.01250.0982-0.00580.05534.303-10.06871.0672
186.59620.84791.3430.1025-0.55910.72080.0384-0.004-0.0151-0.1325-0.0460.01970.2504-0.07410.00750.1102-0.0072-0.01380.1065-0.00260.0013-13.8615-4.9786-10.4395
195.5122-0.49520.32112.2668-0.00620.0379-0.0078-0.06460.19970.0959-0.0267-0.13850.01210.15360.03450.078-0.01090.01350.05140.02590.11573.22594.3409-3.0309
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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