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

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Basic information

Entry
Database: PDB / ID: 4epj
TitleCrystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate p2-NC
Components
  • protease, tethered dimer
  • substrate p2-NC
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
ACETATE ION / 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: 1.69 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 17, 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: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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
D: substrate p2-NC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3758
Polymers22,9132
Non-polymers4626
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-6 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.001, 58.816, 61.794
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

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Protein / Protein/peptide , 2 types, 2 molecules AD

#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 p2-NC


Mass: 908.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthetic peptide corresponding to p2-NC cleavage site (HIV-1 protease)
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YP46

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Non-polymers , 6 types, 74 molecules

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


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 39.18 %
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: 1.66→50 Å / Num. obs: 21538 / % possible obs: 95.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.049 / Χ2: 1.037 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.66-1.726.20.69512221.027155.7
1.72-1.797.10.52322101.0191100
1.79-1.877.30.33122361.0611100
1.87-1.977.30.19922221.0461100
1.97-2.097.30.1322351.0381100
2.09-2.257.30.09622461.0281100
2.25-2.487.30.07422401.0291100
2.48-2.847.20.05822781.0241100
2.84-3.587.10.05322801.041100
3.58-506.60.02823691.048197.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→42.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2627 / WRfactor Rwork: 0.2175 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8372 / SU B: 5.463 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1196 / SU Rfree: 0.1124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 1101 5.1 %RANDOM
Rwork0.1978 ---
obs0.1993 21488 99.46 %-
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: 74.44 Å2 / Biso mean: 36.0475 Å2 / Biso min: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20 Å2
2---0.74 Å20 Å2
3---3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.69→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 28 68 1618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191647
X-RAY DIFFRACTIONr_bond_other_d0.0010.021082
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9932248
X-RAY DIFFRACTIONr_angle_other_deg0.87932675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45625.47253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47415271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.49156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
LS refinement shellResolution: 1.685→1.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 75 -
Rwork0.295 1321 -
all-1396 -
obs--96.88 %
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)
14.54830.03060.08430.678-0.58951.9021-0.0742-0.725-0.42410.37790.19-0.1126-0.0760.0528-0.11580.31810.1112-0.07580.2618-0.00560.09733.4941-0.069630.4493
29.3026-0.08354.08825.2826-4.1735.2661-0.0655-0.18570.5682-0.00020.01230.63960.1376-0.13540.05320.1422-0.02450.21430.0909-0.0850.467-13.5522-1.229422.79
37.33222.1207-3.43683.3878-0.71231.6406-0.1048-0.0947-0.30020.2058-0.07150.20480.08370.03020.17630.1535-0.01410.04140.1210.00210.0533-5.1465-1.752422.2965
47.59367.00251.72977.24882.48451.4759-0.02070.1398-0.0767-0.09780.00370.0214-0.03-0.070.0170.12310.0313-0.0220.1133-0.01530.105-4.5458-0.399713.5096
515.6437-2.6618-0.16934.2271-3.80393.89830.29450.61990.0782-0.26580.09410.36320.2035-0.2548-0.38850.12780.0328-0.0440.1999-0.06050.0833-15.4419-0.38527.0841
613.9672-2.56933.85292.1425-2.843310.06930.0979-0.1294-0.0167-0.04890.1701-0.0961-0.0239-0.0859-0.26810.17910.03870.03660.1041-0.00110.04812.3414-1.0046.154
72.1145-0.736-0.31551.98531.00152.84380.10040.26220.1371-0.1434-0.18410.28890.006-0.27850.08370.09380.0082-0.00730.09490.02750.0935-8.8261.61239.6631
85.9659-1.5269-0.62744.5173-0.06024.5886-0.1047-0.20590.02240.2155-0.02350.334-0.25380.10390.12820.0714-0.00940.02840.03460.01020.1118-10.83077.714121.6384
91.2182-0.09720.553.41820.79381.8415-0.04740.0750.07140.0581-0.00440.10740.1126-0.01480.05170.0880.00980.03090.07840.00540.0229-3.10663.97317.9409
1013.6073-2.146311.46450.6741-3.384417.0789-0.2060.11460.50120.1529-0.1407-0.0572-0.7420.88240.34680.2424-0.0167-0.0510.1572-0.03590.03779.176613.542827.8228
113.79331.4401-0.34892.92741.33160.9425-0.0450.15860.0375-0.1160.0798-0.1394-0.0701-0.0124-0.03480.14360.0001-0.02340.05870.04080.17074.232412.526816.9507
123.396-0.28350.8330.988-0.10640.3943-0.06290.32030.375-0.04860.0157-0.34130.00160.14630.04720.12640.00370.0140.15620.0040.186317.2366.122217.794
1315.3012.576-13.7954.3531-3.444613.5238-0.14950.19790.0578-0.30920.1964-0.04370.358-0.0141-0.04690.09630.014-0.0150.1051-0.01750.057416.3323-2.75414.9648
1414.35194.5671.493412.3686-8.070210.67790.01110.491-0.48020.4233-0.1007-0.5129-0.53550.33460.08960.0281-0.0134-0.00490.1572-0.09430.090927.6468-6.663413.8897
1515.8710.39582.05555.89512.62281.3909-0.0587-0.4323-0.54380.19050.3304-0.47670.06850.0836-0.27160.11260.0241-0.01580.1290.01460.097915.9932-13.284114.8752
1611.4837-1.97651.973.06881.78422.02120.09910.2578-0.0968-0.18670.0951-0.2728-0.12180.0967-0.19420.10630.00250.02130.1211-0.03420.110214.3324-9.088612.1671
174.7682-2.70760.85676.89743.29692.8792-0.18510.05740.37310.1463-0.0365-0.1927-0.06880.04810.22160.1282-0.0171-0.13320.21060.02320.358122.77442.965425.7847
182.8611-0.8736-0.81812.92672.58742.66030.15220.17270.1512-0.3120.1304-0.4409-0.2510.0039-0.28260.07310.0080.05210.1082-0.0330.121416.904-1.788915.9015
194.12920.83983.08773.91272.11872.9083-0.068-0.14550.06670.27490.12-0.27690.0349-0.0375-0.0520.16030.0099-0.05370.1556-0.02810.080913.2790.282327.2263
2013.9526-11.7172-1.027418.1753-1.41514.4182-0.4372-0.44330.11650.91130.34020.50320.1447-0.46040.0970.20130.05530.01930.1469-0.05780.07423.11217.661129.9963
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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