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- PDB-4f76: Crystal Structure of the active HIV-1 Protease in Complex with th... -

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Basic information

Entry
Database: PDB / ID: 4f76
TitleCrystal Structure of the active HIV-1 Protease in Complex with the products of p1-p6 substrate
Components
  • C terminal product of substrate p1-p6
  • N terminal product of substrate p1-p6
  • Protease
Keywordshydrolase/hydrolase product / HIV-1 protease / substrate complex / AIDS / product complex / Aspartyl protease / HYDROLASE / hydrolase-hydrolase product complex
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSchiffer, C.A. / Nalam, M.N.L. / Mittal, S.
CitationJournal: To be Published
Title: Crystal Structure of the active HIV-1 Protease in Complex with the products of p1-p6 substrate
Authors: Mittal, S. / Nalam, M.N.L. / Schiffer, C.A.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
C: N terminal product of substrate p1-p6
D: C terminal product of substrate p1-p6


Theoretical massNumber of molelcules
Total (without water)22,7954
Polymers22,7954
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-30 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.906, 58.367, 61.928
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


Mass: 10801.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide N terminal product of substrate p1-p6


Mass: 590.652 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: N-terminal of the synthetic peptide corresponding to p1-p6 cleavage site
Source: (synth.) Human immunodeficiency virus 1
#3: Protein/peptide C terminal product of substrate p1-p6


Mass: 600.688 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: C-terminal of the synthetic peptide corresponding to p1-p6 cleavage site
Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 39.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-31% 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: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 16269 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.062 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.926.60.38415891.0991100
1.92-1.996.60.26916071.0751100
1.99-2.086.50.19315991.0681100
2.08-2.196.50.15915971.0421100
2.19-2.336.50.12416091.0871100
2.33-2.516.50.10316151.0571100
2.51-2.766.50.07816341.0451100
2.76-3.166.40.06516311.027199.9
3.16-3.996.20.05616571.053199.8
3.99-505.80.03217311.066197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1981 / WRfactor Rwork: 0.1691 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8926 / SU B: 4.831 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1387 / SU Rfree: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 810 5 %RANDOM
Rwork0.1671 ---
obs0.1685 16148 99.28 %-
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: 64.71 Å2 / Biso mean: 26.2493 Å2 / Biso min: 13.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 0 90 1631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221613
X-RAY DIFFRACTIONr_bond_other_d0.0010.021083
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9842199
X-RAY DIFFRACTIONr_angle_other_deg0.83732675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.45825.08559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25715276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.507158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 62 -
Rwork0.183 1113 -
all-1175 -
obs--99.32 %
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)
15.30324.7659-4.33289.6927-3.66354.6005-0.15940.3682-0.1778-0.5420.042-0.10710.02380.01420.11740.1751-0.0305-0.01210.1777-0.03880.073120.77941.1449-1.6293
229.0308-0.05520.88042.6741-0.36730.0811-0.09430.0793-0.606-0.13660.0788-0.060.04130.00230.01550.20180.01080.04420.1197-0.01530.113127.4191-3.56694.6095
319.4213-6.354410.67797.55112.321312.0510.30080.62210.2353-0.30230.0937-0.5987-0.07440.6388-0.39450.17320.01370.09440.15230.05550.341141.6388-0.84429.0961
429.9441-9.45220.00957.09710.94150.36550.0388-0.1229-0.5962-0.1972-0.0356-0.2170.1596-0.0813-0.00310.3348-0.01990.09220.138-0.01870.150532.323-3.21777.6139
54.84280.21752.70383.83840.01177.6175-0.0111-0.31-0.0220.22310.1289-0.08690.1219-0.0588-0.11770.08210.00210.01310.0738-0.00150.079623.59014.79815.083
612.8965-8.82010.076930.613-6.88435.7524-0.1142-0.2483-0.5960.0655-0.0446-0.29580.34820.1650.15880.0782-0.0248-0.00420.0962-0.00130.071332.9439-3.495217.394
75.7465-1.0875-2.89858.27038.2229.8802-0.0288-0.2970.0978-0.16250.193-0.57-0.2120.7321-0.16430.07370.0132-0.04660.24010.11090.233542.2473-0.794521.9903
812.92124.08841.36033.75491.01573.0516-0.0178-0.20050.06350.16170.0373-0.0202-0.09390.0251-0.01950.1291-0.0167-0.00390.0927-0.00630.067125.8665-0.455326.1397
99.64834.5254-4.84423.658-2.32464.77920.1438-0.1987-0.06690.2945-0.1768-0.1634-0.00630.29750.0330.1154-0.0052-0.03150.1119-0.01530.073330.6119-1.300226.5173
104.94912.5961-1.8964.2857-4.48710.4910.0505-0.41890.09070.185-0.1906-0.1754-0.21560.37440.14020.0688-0.012-0.02650.1166-0.01320.16440.15336.591818.6478
1111.0164-1.65610.03338.699-7.102726.57590.0220.6545-0.143-0.52030.0387-0.305-0.04030.2647-0.06080.09150.01150.05620.0655-0.03690.102236.3025.65814.4584
123.6871.00853.02466.3657-1.91025.8509-0.1285-0.00650.0849-0.0988-0.0602-0.374-0.02210.28420.18860.05750.00120.00650.0707-0.01520.136237.39488.365513.1679
135.62923.65852.98027.0177-0.20352.9090.0853-0.0139-0.12820.0166-0.0220.09330.27690.026-0.06330.14090.00540.02970.10770.00650.10230.0593-4.763819.1634
142.1795-2.5713-0.92216.49351.63942.4325-0.0234-0.014-0.10350.1378-0.00230.0020.08190.0780.02570.0665-0.00840.00610.0766-0.00020.077928.1863.800513.4439
155.74362.21332.77015.02031.64362.1233-0.10110.1320.1152-0.19730.1124-0.139-0.09510.0523-0.01120.0628-0.00620.01420.06190.00230.081430.463310.6558.9705
1613.3645.13215.38045.3892.47937.0373-0.4285-0.04440.329-0.29460.07440.2639-0.2427-0.25460.35420.1408-0.02-0.00810.09080.00050.062818.547910.47562.843
175.9643.74685.02923.31191.57929.1577-0.27750.05050.512-0.4992-0.02020.323-0.3343-0.17860.29770.32630.0538-0.03150.1490.02060.213920.359514.81087.5533
1823.44090.33073.66421.71520.94915.41-0.1749-0.70730.39190.37250.2010.2284-0.304-0.1722-0.0260.19780.04390.01570.1079-0.01030.16115.967411.383514.4687
1918.9778.8397-1.230112.90980.85283.9631-0.17520.28730.4997-0.47370.04990.83130.0499-0.34170.12530.09040.0258-0.01760.1367-0.01660.13321.10586.440711.1818
2018.4823-6.97290.72215.94541.601510.5079-0.0221-0.73490.36880.40420.00770.37460.0213-0.45560.01440.0984-0.03460.08290.2358-0.07730.1663.71477.900515.6129
216.6305-0.5667-0.34584.90461.79682.557-0.0167-0.1187-0.05870.12510.0539-0.13730.0713-0.0173-0.03720.0778-0.01690.00020.06280.00850.066817.03862.60910.6984
2214.1735-2.9124-11.27574.3131.806415.3368-0.0944-0.0914-0.04770.14520.09680.09360.0448-0.0303-0.00240.0861-0.0303-0.02770.06030.02430.098310.4505-2.61314.0429
2320.405814.85416.397114.640613.550416.8150.6643-0.49690.27210.187-0.58320.94520.2141-0.6237-0.08110.19350.00670.01230.2840.07070.3544-1.3494-2.951919.0254
2411.9755-6.87645.71896.1750.18678.15250.1003-0.3636-0.6308-0.01830.03860.46580.1433-0.457-0.13890.1103-0.0632-0.03650.15620.11950.20922.5657-12.894915.8725
2516.654311.56575.485610.44044.71724.6844-0.063-0.05370.06590.14580.05790.0542-0.1965-0.0780.00510.0978-0.0062-0.00350.08930.00710.084918.1622-8.716319.7887
269.44420.05893.19112.9047-1.91272.4310.0597-0.3408-0.1871-0.00010.15930.16680.0659-0.175-0.2190.1053-0.0107-0.00210.10480.00870.11179.579-10.439519.3945
278.9106-3.56253.8711.7547-9.501610.79470.3050.1833-0.5725-0.5991-0.10770.1880.29820.075-0.19730.086-0.0525-0.0210.12640.040.13460.6357-5.94518.6304
287.15573.395-3.820412.8529-6.239212.40930.0728-0.03570.28410.0025-0.19010.1209-0.3412-0.02870.11740.1176-0.0246-0.03790.07630.01130.11024.96937.63764.6562
292.8464-2.83534.86898.7653-7.17129.49850.0218-0.0387-0.1379-0.0580.17280.37670.0453-0.2613-0.19470.0978-0.0215-0.00040.1452-0.00580.14263.5708-1.48995.1825
302.76950.6336-3.07455.2014-0.28376.31570.0139-0.4981-0.1060.4295-0.0434-0.0601-0.46380.36840.02950.1596-0.0192-0.00050.18180.04520.12199.116-3.46220.1758
315.1587-1.3267-4.60336.13424.39278.13590.0508-0.30480.06390.25310.07530.14330.17540.1836-0.12610.0952-0.0167-0.00020.07850.02930.075612.82640.842512.2165
323.99530.01822.71855.9271-1.46962.2222-0.17660.10020.0745-0.21950.20290.2282-0.0440.0009-0.02630.1536-0.051-0.03680.19140.03560.101810.79710.9522.4077
3321.42544.60572.25765.3444-0.32365.0801-0.35040.2483-0.0218-0.43940.269-0.2136-0.03810.27270.08140.1382-0.02660.00450.0991-0.00310.047422.91417.38570.7609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 12
3X-RAY DIFFRACTION3A13 - 18
4X-RAY DIFFRACTION4A19 - 24
5X-RAY DIFFRACTION5A25 - 30
6X-RAY DIFFRACTION6A31 - 35
7X-RAY DIFFRACTION7A36 - 42
8X-RAY DIFFRACTION8A43 - 52
9X-RAY DIFFRACTION9A53 - 58
10X-RAY DIFFRACTION10A59 - 63
11X-RAY DIFFRACTION11A64 - 69
12X-RAY DIFFRACTION12A70 - 75
13X-RAY DIFFRACTION13A76 - 82
14X-RAY DIFFRACTION14A83 - 88
15X-RAY DIFFRACTION15A89 - 94
16X-RAY DIFFRACTION16A95 - 99
17X-RAY DIFFRACTION17B1 - 6
18X-RAY DIFFRACTION18B7 - 11
19X-RAY DIFFRACTION19B12 - 17
20X-RAY DIFFRACTION20B18 - 22
21X-RAY DIFFRACTION21B23 - 28
22X-RAY DIFFRACTION22B29 - 34
23X-RAY DIFFRACTION23B35 - 39
24X-RAY DIFFRACTION24B40 - 45
25X-RAY DIFFRACTION25B46 - 52
26X-RAY DIFFRACTION26B53 - 58
27X-RAY DIFFRACTION27B59 - 63
28X-RAY DIFFRACTION28B64 - 69
29X-RAY DIFFRACTION29B70 - 75
30X-RAY DIFFRACTION30B76 - 81
31X-RAY DIFFRACTION31B82 - 87
32X-RAY DIFFRACTION32B88 - 94
33X-RAY DIFFRACTION33B95 - 99

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