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- PDB-5yrs: X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrah... -

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Basic information

Entry
Database: PDB / ID: 5yrs
TitleX-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrahedral Intermediate and Its SIHB with Catalytic Aspartate
Components
  • (PROTEASE) x 2
  • RT-RH oligopeprtide
KeywordsHYDROLASE / HIV-1 PROTEASE / TETRAHEDRAL INTERMEDIATE / SHORT IONIC HYDROGEN BOND / SUBSTRATE COMPLEX / RT-RH
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 / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / 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 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDas, A. / Mahale, S. / Prashar, V. / Bihani, S. / Ferrer, J.-L. / Hosur, M.V.
Funding support India, 1items
OrganizationGrant numberCountry
DAEInternal India
CitationJournal: J. Am. Chem. Soc. / Year: 2010
Title: X-ray snapshot of HIV-1 protease in action: observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate.
Authors: Das, A. / Mahale, S. / Prashar, V. / Bihani, S. / Ferrer, J.L. / Hosur, M.V.
History
DepositionNov 10, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 7, 2018ID: 3MIM
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASE
B: PROTEASE
X: RT-RH oligopeprtide


Theoretical massNumber of molelcules
Total (without water)23,0413
Polymers23,0413
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-31 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.560, 62.560, 81.860
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 PROTEASE / RETROPEPSIN / PR


Mass: 11163.094 Da / Num. of mol.: 1 / Mutation: C95M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: M:B_HXB2R / Gene: gag-pol, HIV-1 PR B / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin
#2: Protein PROTEASE / RETROPEPSIN / PR


Mass: 11102.976 Da / Num. of mol.: 1 / Mutation: C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: M:B_HXB2R / Gene: gag-pol, HIV-1 PR B / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin
#3: Protein/peptide RT-RH oligopeprtide


Mass: 774.815 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE CORRESPONDS TO RT-RH CLEAVAGE SITE, NATURALLY OCCURING IN HIV-1 GAG-POL POLYPROTEIN.
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHOR STATES THAT RESIDUE HPH X 4 IS L-PHENYLALANINE AND HYDRATED L-PHE RESIDUE HAVING ...THE AUTHOR STATES THAT RESIDUE HPH X 4 IS L-PHENYLALANINE AND HYDRATED L-PHE RESIDUE HAVING TETRAHEDRAL CARBON CA AND THE O AND OXT ARE THE TWO HYDROXYL GROUPS ATTACHED TO THE CA IN CASE OF HPH. THUS THE BOND CONNECTING CA (HPH) TO N (TYR) IS NOT A PLANAR PEPTIDYL BOND.

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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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M PHOSPHATE-0.2M CITRATE BUFFER, AMM. SULPHATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2008
RadiationMonochromator: A HORIZONTALLY DIFFRACTING SI (111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 17226 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.76
Reflection shellResolution: 1.76→1.81 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.98 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LV1

1lv1


Resolution: 1.76→50 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.25 843 RANDOM
Rwork0.223 --
obs0.223 16819 -
Refinement stepCycle: 1 / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 0 194 1783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.99
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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