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- PDB-4ep3: Crystal Structure of inactive single chain wild-type HIV-1 Protea... -

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Basic information

Entry
Database: PDB / ID: 4ep3
TitleCrystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate CA-p2
Components
  • protease, tethered dimer
  • substrate CA-p2
Keywordshydrolase/hydrolase substrate / HIV-1 protease / specificity design / drug design / Protease inhibitors / AIDS / Aspartyl protease / HYDROLASE / hydrolase-hydrolase substrate complex
Function / homology
Function and homology information


viral budding via host ESCRT complex / RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...viral budding via host ESCRT complex / RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm
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. / Integrase-like, N-terminal ...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. / 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
BETA-MERCAPTOETHANOL / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSchiffer, C.A. / Mittal, S.
CitationJournal: Protein Sci. / Year: 2012
Title: Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.
Authors: Alvizo, O. / Mittal, S. / Mayo, S.L. / Schiffer, C.A.
History
DepositionApr 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 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 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: protease, tethered dimer
E: substrate CA-p2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3506
Polymers22,9952
Non-polymers3544
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.046, 58.935, 61.451
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein protease, tethered dimer /


Mass: 22005.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide substrate CA-p2


Mass: 990.220 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide representing CA-p2 cleavage site (HIV-1 protease)
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YP46
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 17300 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.068 / Χ2: 1.048 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.81-1.8770.47316741.12199.8
1.87-1.9570.30917151.019199.8
1.95-2.047.10.20917071.013199.8
2.04-2.157.10.15616831.039199.9
2.15-2.287.10.12517241.0041100
2.28-2.467.10.117221.0431100
2.46-2.77.10.08217201.0321100
2.7-3.097.10.07217531.0911100
3.09-3.96.80.06317621.031199.9
3.9-506.50.04518401.094198.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→42.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.256 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 877 5.1 %RANDOM
Rwork0.1886 ---
obs0.1905 17243 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.69 Å2 / Biso mean: 34.666 Å2 / Biso min: 9.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2---0.74 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.81→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 22 62 1626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191626
X-RAY DIFFRACTIONr_bond_other_d0.0010.021080
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9882213
X-RAY DIFFRACTIONr_angle_other_deg0.8332669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8772554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89315268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.782157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
LS refinement shellResolution: 1.814→1.861 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 48 -
Rwork0.218 1045 -
all-1093 -
obs--95.88 %
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)
17.37-1.25430.37815.29321.30282.7376-0.2742-0.5391-0.37360.63780.35980.17830.1811-0.0577-0.08560.19430.05210.03770.17520.06140.03153.4123-0.593830.4145
213.4771-0.79847.30913.6997-1.70818.7351-0.3384-0.19490.36120.1172-0.17561.14170.3388-0.27680.51410.1198-0.03550.11030.083-0.0930.5036-13.8897-1.406622.6836
36.1386-0.2824-4.55350.07680.23613.3891-0.23220.0642-0.30970.043-0.03590.11980.181-0.06320.26810.1262-0.00950.06690.0778-0.03480.194-5.197-1.470922.0693
49.62479.0971.49829.09832.00110.9306-0.05280.189-0.1345-0.12060.0132-0.0503-0.0634-0.15640.03960.14540.0287-0.03340.119800.0988-4.6878-0.626913.4779
59.5694-2.9588-1.59562.6068-2.50995.60280.28620.78910.1945-0.1323-0.05840.05520.0232-0.4957-0.22770.07910.0275-0.03250.1832-0.03260.0668-15.4938-0.65247.0711
69.1066-0.75396.36833.1339-2.20478.6620.14340.23660.0870.09430.0413-0.09390.07240.2192-0.18470.11240.0532-0.00680.1048-0.02520.03432.308-1.23696.1693
72.772-1.8636-0.59923.33042.20463.99240.22480.34530.1085-0.3254-0.33820.4371-0.0861-0.43820.11340.0797-0.0032-0.04180.10090.02010.171-9.07251.528810.1845
86.5943-4.5196-0.11325.50561.1927.6019-0.2951-0.3159-0.07520.1273-0.08950.3743-0.6828-0.02720.38460.09580.0072-0.00850.07680.00170.1597-10.98127.746821.5414
91.86850.61641.03574.00830.89552.4482-0.01650.02910.07650.1019-0.01820.2510.0191-0.01690.03460.05530.0190.0210.04170.01140.0229-3.21583.889817.8647
101.5151-2.76566.2685.1054-11.529826.0969-0.24530.24490.17670.5186-0.3613-0.2363-1.24341.07330.60660.3334-0.0613-0.10670.3046-0.14050.29288.837913.639627.6376
1110.6916-2.9779-1.47343.0574-0.26810.4274-0.05220.54520.05930.0227-0.0806-0.2908-0.0161-0.10620.13290.14690.0118-0.01740.0461-0.03610.14623.844112.475816.5948
125.6526-1.55960.42862.8509-0.99661.13920.14420.34450.74670.0414-0.1515-0.49920.00050.20450.00730.07630.00150.0220.10470.01530.16917.09676.255717.5604
1320.71623.94-15.59313.6827-3.558417.2666-0.21320.58590.0588-0.18410.2477-0.20680.3558-0.1608-0.03450.06710.02250.01140.0677-0.01910.024116.3017-2.706214.9073
149.75975.97451.265310.4113-6.20927.3883-0.02560.481-0.44910.2275-0.2301-0.5835-0.26440.5820.25570.11970.01440.01940.2561-0.08050.127327.7423-6.635314.0264
1517.9225-2.33970.97694.67752.18711.2795-0.1017-0.6411-0.36040.3580.2687-0.23860.17480.0515-0.1670.13710.0214-0.04350.12350.01650.034116.0952-13.27415.0095
1614.89540.27284.0911.61251.62192.61380.03840.34650.0013-0.12750.0636-0.1202-0.11770.1376-0.1020.11560.0183-0.00590.102-0.0070.058214.6747-9.439911.9187
174.0441-2.61180.87026.87441.7294.3039-0.1559-0.25140.42040.31620.0085-0.2955-0.17270.23750.14740.066-0.0019-0.04020.1056-0.07580.140622.6613.421625.6244
183.7584-1.5305-1.59662.75990.97630.73090.12930.11960.2277-0.26350.0301-0.3244-0.0828-0.0376-0.15940.10430.00940.00380.0736-0.0020.085716.8571-1.71415.8469
1910.2144-1.12673.49421.41371.42245.3662-0.1867-0.50190.21660.15060.1649-0.2882-0.26960.01870.02180.1410.0286-0.08990.1243-0.02260.126813.14540.464527.1517
2028.9214-10.5349-4.14059.7585.00054.5606-0.3242-0.15170.7840.76560.3192-0.12770.0343-0.20410.0050.25620.09640.0030.17820.00820.02692.85217.812329.8985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION2A11 - 18
3X-RAY DIFFRACTION3A19 - 26
4X-RAY DIFFRACTION4A27 - 35
5X-RAY DIFFRACTION5A36 - 45
6X-RAY DIFFRACTION6A46 - 50
7X-RAY DIFFRACTION7A51 - 66
8X-RAY DIFFRACTION8A67 - 75
9X-RAY DIFFRACTION9A76 - 97
10X-RAY DIFFRACTION10A98 - 104
11X-RAY DIFFRACTION11A105 - 109
12X-RAY DIFFRACTION12A110 - 128
13X-RAY DIFFRACTION13A129 - 135
14X-RAY DIFFRACTION14A136 - 142
15X-RAY DIFFRACTION15A143 - 148
16X-RAY DIFFRACTION16A149 - 159
17X-RAY DIFFRACTION17A160 - 170
18X-RAY DIFFRACTION18A171 - 185
19X-RAY DIFFRACTION19A186 - 194
20X-RAY DIFFRACTION20A195 - 199

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