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- PDB-3phv: X-RAY ANALYSIS OF HIV-1 PROTEINASE AT 2.7 ANGSTROMS RESOLUTION CO... -

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Entry
Database: PDB / ID: 3phv
TitleX-RAY ANALYSIS OF HIV-1 PROTEINASE AT 2.7 ANGSTROMS RESOLUTION CONFIRMS STRUCTURAL HOMOLOGY AMONG RETROVIRAL ENZYMES
ComponentsUNLIGANDED HIV-1 PROTEASE
KeywordsHYDROLASE / ASPARTIC PROTEINASE
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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / host multivesicular body / protein processing / 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 / 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 / viral translational frameshifting / lipid binding / symbiont entry into host cell / 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 speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsLapatto, R. / Blundell, T.L. / Hemmings, A. / Wilderspin, A. / Wood, S.P. / Danley, D.E. / Geoghegan, K.F. / Hawrylik, S.J. / Hobart, P.M.
Citation
Journal: Nature / Year: 1989
Title: X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes.
Authors: Lapatto, R. / Blundell, T. / Hemmings, A. / Overington, J. / Wilderspin, A. / Wood, S. / Merson, J.R. / Whittle, P.J. / Danley, D.E. / Geoghegan, K.F. / Hawrylik, S.J. / Lee, S.E. / Scheld, K.G. / Hobart, P.M.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Crystallization of the Aspartyl Protease from the Human Immunodeficiency Virus, HIV-1
Authors: Mckeever, B.M. / Navia, M.A. / Fitzgerald, P.M.D. / Springer, J.P. / Leu, C.-T. / Heimbach, J.C. / Herber, W.K. / Sigal, I.S. / Darke, P.L.
History
DepositionNov 4, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINAL STRANDS FROM BOTH ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINAL STRANDS FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTI-PARALLEL BETA-SHEET, S2. APPLICATION OF THE TWO-FOLD ROTATION TO RESIDUES 1 TO 5 AND 95 TO 99 GENERATES RESIDUES 1' TO 5' AND 95' TO 99' RESPECTIVELY. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. STRANDS 1 AND 3 ARE FROM THE MOLECULE IN THIS ENTRY AND STRANDS 2 AND 4 ARE FROM THE SYMMETRY RELATED MOLECULE. 1 S2 4 PRO 1 LEU 5 0 2 S2 4 CYS 95' PHE 99'-1 3 S2 4 CYS 95 PHE 99 -1 4 S2 4 PRO 1' LEU 5'-1

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UNLIGANDED HIV-1 PROTEASE


Theoretical massNumber of molelcules
Total (without water)10,8041
Polymers10,8041
Non-polymers00
Water00
1
A: UNLIGANDED HIV-1 PROTEASE

A: UNLIGANDED HIV-1 PROTEASE


Theoretical massNumber of molelcules
Total (without water)21,6082
Polymers21,6082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2980 Å2
ΔGint-18 kcal/mol
Surface area10330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.240, 50.240, 107.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UNLIGANDED HIV-1 PROTEASE


Mass: 10803.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Cell line: S2 / Gene: POL / Organ: LEAVES / Gene (production host): POL / Production host: Escherichia coli (E. coli) / References: UniProt: P04585

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
2100 mMimidazole/HCl1dropor NaMOPS/MOPS
3250 mM1dropNaCl
410 mMDTT1drop
53 mM1dropNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 2200 / Observed criterion σ(I): 2 / Num. measured all: 10000 / Rmerge(I) obs: 0.11

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.7→10 Å / σ(I): 3 /
RfactorNum. reflection
Rwork0.191 -
obs-2370
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 0 0 758
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 2370 / σ(I): 3 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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