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- PDB-4ep2: Crystal Structure of inactive single chain wild-type HIV-1 Protea... -

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Basic information

Entry
Database: PDB / ID: 4ep2
TitleCrystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate RT-RH
Components
  • protease, tethered dimer
  • substrate RT-RH
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


: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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 / 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
PHOSPHATE ION / Gag-Pol polyprotein / Pol protein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Assembly

Deposited unit
A: protease, tethered dimer
B: substrate RT-RH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0934
Polymers22,9062
Non-polymers1872
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.205, 58.690, 61.792
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 RT-RH


Mass: 900.929 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: this peptide represents the RT-RH substrate cleavage site for HIV protease
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YV20
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.03 Å3/Da / Density % sol: 39.46 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 13957 / % possible obs: 91.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.079 / Χ2: 1.035 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.975.60.31810631.371171.8
1.97-2.056.70.26714921.077199.9
2.05-2.146.80.20514860.9691100
2.14-2.256.30.17611641.028177.6
2.25-2.396.70.13412370.944183.6
2.39-2.586.90.11315281.0481100
2.58-2.8470.08915161.0491100
2.84-3.256.90.06715191.0811100
3.25-4.096.10.05813130.953184.7
4.09-506.60.03716390.946199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.56 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2492 / WRfactor Rwork: 0.1968 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.772 / SU B: 9.874 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2279 / SU Rfree: 0.1928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 701 5 %RANDOM
Rwork0.2061 ---
obs0.2089 13906 91.58 %-
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: 43.99 Å2 / Biso mean: 23.05 Å2 / Biso min: 4.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 11 115 1684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191746
X-RAY DIFFRACTIONr_bond_other_d0.0010.021162
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9852387
X-RAY DIFFRACTIONr_angle_other_deg0.83332876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3495228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.91724.92163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81715296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.406158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211935
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02321
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.547 30 -
Rwork0.34 574 -
all-604 -
obs--57.91 %
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)
15.7114-0.14160.62412.9591-0.85974.3622-0.0260.0921-0.21020.08430.04470.45330.1978-0.0222-0.01870.06310.0039-0.00650.0145-0.01960.130819.082416.056919.6388
211.9366-2.33353.68784.0199-1.75071.44110.00390.0704-0.23270.1483-0.0091-0.1215-0.03490.00570.00520.0246-0.04590.02850.20710.00090.23711.185722.28717.5511
36.19622.6698-0.92852.71650.35390.5038-0.00260.4705-0.058-0.1046-0.21030.43-0.0581-0.27530.21290.08660.030.00030.1941-0.06020.220910.512323.122316.202
410.47481.01876.48211.8926-0.9768.2811-0.08370.19720.0699-0.23570.11950.1932-0.286-0.1681-0.03580.11110.0164-0.00130.04320.00120.119410.377231.542915.0258
54.83713.0158-1.56523.05851.11294.21270.3250.25680.4770.2410.03670.1807-0.0249-0.286-0.36170.07630.0444-0.0280.15890.06810.22970.862438.924614.4513
610.715-13.0672-1.49816.09792.09947.2256-0.59460.1113-0.65940.6458-0.00020.66970.35480.11120.59480.1735-0.05530.12010.1568-0.11320.26217.475738.785211.9402
75.59691.953-1.79723.3885-3.33933.30420.05930.03850.1175-0.14870.22770.32130.1362-0.2153-0.2870.0754-0.0187-0.02780.0546-0.00950.1386.021835.432216.3606
81.5063-2.9027-1.410414.8769-3.33455.2884-0.1277-0.0069-0.05070.4242-0.0008-0.1405-0.00640.00790.12850.0143-0.0079-0.00520.1550.01750.22794.605226.286925.3694
91.7301-0.87570.44771.4988-0.70830.3413-0.0112-0.0482-0.0323-0.06660.07140.19410.041-0.034-0.06020.08480.00950.02160.0612-0.00580.129912.191528.874720.525
1012.3286-8.681-3.525928.27499.37325.12920.0238-0.8009-0.31260.58230.2192-0.56140.37810.6209-0.24290.15360.05710.01150.22660.03190.060524.753522.7232.4888
1111.7093.7344-6.22117.9967-0.25387.06130.12240.13810.27740.23830.04690.2005-0.4648-0.1717-0.16930.09030.04060.00230.0994-0.00890.014419.165932.63728.0879
123.13630.71060.66062.98421.0211.7298-0.0623-0.24380.11310.0428-0.0225-0.177-0.13750.06520.08480.06910.0027-0.00850.06490.01170.03633.798730.874922.8978
138.20099.4107-2.001312.6783-1.02461.5865-0.29680.33290.0366-0.57820.21060.0636-0.0776-0.03930.08620.0890.0286-0.01740.13660.04910.034231.341130.557813.1187
145.7436-5.0963-5.013510.002513.022222.4538-0.1054-0.2607-0.04310.14060.3318-0.17850.41681.0179-0.22640.0626-0.0043-0.01920.14250.03360.032543.044629.65928.2927
1524.9374-4.9455-2.74571.02560.21822.94930.07750.6270.0686-0.048-0.11050.0020.0612-0.06710.0330.1695-0.0397-0.07380.05020.0280.1430.784727.94372.9988
1617.0304-6.36831.883.7095-2.22142.82540.14520.2034-0.0263-0.0591-0.07450.1885-0.03650.0315-0.07070.11460.0060.02740.02160.00580.058229.557431.08856.0861
175.4671-0.0572-3.04241.82490.449311.3336-0.0637-0.2347-0.22250.1721-0.1491-0.11590.39130.36050.21280.06380.00480.00860.03570.02570.029838.17822.422221.7117
181.5803-0.5453-0.41151.488-1.54312.33610.07690.07030.0345-0.0685-0.0985-0.0171-0.03320.08240.02170.11310.0048-0.02760.05880.00520.025232.127629.849314.4006
196.49980.34861.03981.40630.62991.0889-0.07110.0878-0.36950.09420.07440.3342-0.25090.1793-0.00330.1451-0.02530.05760.062-0.01390.125829.032319.63319.5557
2018.8877-0.3989-12.1890.74571.592110.5186-0.4146-0.1276-0.1760.04760.04420.15440.1538-0.06720.37030.22270.120.02670.21880.05650.094218.885418.689427.5164
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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