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- PDB-3dox: X-ray structure of HIV-1 protease in situ product complex -

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Basic information

Entry
Database: PDB / ID: 3dox
TitleX-ray structure of HIV-1 protease in situ product complex
Components
  • A PEPTIDE SUBSTRATE-PIV
  • A PEPTIDE SUBSTRATE-SQNY
  • HIV-1 PROTEASE
KeywordsHYDROLASE / HIV-1 protease / transition state / reaction intermediate / catalysis / inhibitor / X-ray Crystallography / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Host-virus interaction / Lipoprotein / Magnesium / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribosomal frameshifting / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc / Zinc-finger
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / Assembly Of The HIV Virion / exoribonuclease H / exoribonuclease H activity / Budding and maturation of HIV virion / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / peptidase activity / 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 / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein 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. / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHosur, M.V. / Ferrer, J.-L. / Das, A. / Prashar, V. / Bihani, S.
Citation
Journal: Proteins / Year: 2009
Title: X-ray structure of HIV-1 protease in situ product complex
Authors: Bihani, S. / Das, A. / Prashar, V. / Ferrer, J.-L. / Hosur, M.V.
#1: Journal: Proteins / Year: 2001
Title: 1.9 A x-ray study shows closed flap conformation in crystals of tethered HIV-1 PR
Authors: Pillai, B. / Kannan, K.K. / Hosur, M.V.
#2: Journal: Biochem.J. / Year: 2005
Title: Observation of a tetrahedral reaction intermediate in the HIV-1 protease-substrate complex
Authors: Kumar, M. / Prashar, V. / Mahale, S. / Hosur, M.V.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Rapid screening for HIV-1 protease inhibitor leads through X-ray diffraction
Authors: Pillai, B. / Kannan, K.K. / Bhat, S.V. / Hosur, M.V.
#4: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates
Authors: Das, A. / Prashar, V. / Mahale, S. / Serre, L. / Ferrer, J.-L. / Hosur, M.V.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 10, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600Some waters and the short peptide partially occupy the electron density. In some unit cells the ...Some waters and the short peptide partially occupy the electron density. In some unit cells the water cluster is there while in others the ligand is present.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 PROTEASE
P: A PEPTIDE SUBSTRATE-SQNY
Q: A PEPTIDE SUBSTRATE-PIV


Theoretical massNumber of molelcules
Total (without water)22,7413
Polymers22,7413
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.380, 62.380, 82.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HIV-1 PROTEASE / Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid ...Pr160Gag-Pol / Matrix protein p17 / MA / Capsid protein p24 / CA / Spacer peptide p2 / Nucleocapsid protein p7 / NC / Transframe peptide / TF / p6-pol / p6* / Protease / Retropepsin / PR / Reverse transcriptase/ribonuclease H / p66 RT / p51 RT / p15 / Integrase / IN


Mass: 21902.760 Da / Num. of mol.: 1 / Mutation: C95M, C1095A
Source method: isolated from a genetically manipulated source
Details: TETHERED DIMER LINKED BY GGSSG
Source: (gene. exp.) Human immunodeficiency virus type 1 (isolate HXB2 group M subtype B)
Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, HIV-1 retropepsin
#2: Protein/peptide A PEPTIDE SUBSTRATE-SQNY


Mass: 510.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Protein/peptide A PEPTIDE SUBSTRATE-PIV


Mass: 327.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT INCLUDES A LINKER THAT CONSIST OF 996TH GLY, 997TH GLY, 998TH SER, 999TH SER AND 1000TH GLY.

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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: 39.27 %
Crystal growTemperature: 300 K / pH: 6.2
Details: 1-5% saturated ammonium sulfate, pH 6.2, Soaking, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97644 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2006
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97644 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 12272 / Num. obs: 12068 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.03

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
CNSphasing
RefinementResolution: 2→45.11 Å / Occupancy max: 1 / Occupancy min: 0
RfactorNum. reflection% reflection
Rfree0.236 604 4.9 %
Rwork0.197 --
obs0.197 12068 98.3 %
Solvent computationBsol: 77.83 Å2
Displacement parametersBiso mean: 34.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.095 Å2-1.395 Å20 Å2
2---1.095 Å20 Å2
3---2.191 Å2
Refinement stepCycle: LAST / Resolution: 2→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 0 193 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2561.5
X-RAY DIFFRACTIONc_mcangle_it2.2282
X-RAY DIFFRACTIONc_scbond_it1.2462
X-RAY DIFFRACTIONc_scangle_it1.8222.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAMCNS_TOPPAR:DNA-RNA.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAMCNS_TOPPAR:ION.TOP

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