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- PDB-1a94: STRUCTURAL BASIS FOR SPECIFICITY OF RETROVIRAL PROTEASES -

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Basic information

Entry
Database: PDB / ID: 1a94
TitleSTRUCTURAL BASIS FOR SPECIFICITY OF RETROVIRAL PROTEASES
ComponentsPROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HUMAN IMMUNODEFICIENCY VIRUS PROTEASE / ROUS SARCOMA VIRUS PROTEASE / PROTEIN-MEDIATED INTERACTION / VIRAL MATURATION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / 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 / 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 / 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. / 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
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide / Chem-0Q4 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWu, J. / Adomat, J.M. / Ridky, T.W. / Louis, J.M. / Leis, J. / Harrison, R.W. / Weber, I.T.
CitationJournal: Biochemistry / Year: 1998
Title: Structural basis for specificity of retroviral proteases.
Authors: Wu, J. / Adomat, J.M. / Ridky, T.W. / Louis, J.M. / Leis, J. / Harrison, R.W. / Weber, I.T.
History
DepositionApr 16, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASE
B: PROTEASE
D: PROTEASE
E: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6296
Polymers42,9624
Non-polymers1,6662
Water3,261181
1
A: PROTEASE
B: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3143
Polymers21,4812
Non-polymers8331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-30 kcal/mol
Surface area9190 Å2
MethodPISA
2
D: PROTEASE
E: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3143
Polymers21,4812
Non-polymers8331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-30 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.610, 51.940, 61.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1121

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Components

#1: Protein
PROTEASE


Mass: 10740.610 Da / Num. of mol.: 4 / Mutation: Q7K, L33I, K43E, L63I, C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-0Q4 / N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide / Inhibitor analogues of CA-p2


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H70N11O8 / Details: ANALOG OF THE CONSERVED CA-P2 SUBSTRATE
References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPEPTIDE INHIBITOR 0Q4 HAS A REDUCED PEPTIDE (-CH2-NH) INSTEAD OF THE NORMAL PEPTIDE LINK (-CO-NH).
Sequence detailsMUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM ...MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, WHILE RETAINING ACTIVITY SIMILAR TO WILD-TYPE HIV-1 PROTEASE

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growpH: 4.7 / Details: pH 4.7
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.8 mg/mlHIV-1 protease1drop
220 mMsodium acetate1drop
35 mMdithiothreitol1drop
566 mMsodium citrate1reservoir
6132 mMsodium phosphate1reservoir
710 mMdithiothreitol1reservoir
810 %DMSO1reservoir
945 %satammonium sulfate1reservoir
4inhibitor1drop5-fold molar excess

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. obs: 20944 / % possible obs: 86.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.083 / Rsym value: 0.182 / Net I/σ(I): 2
Reflection shellResolution: 2→2.25 Å / Rmerge(I) obs: 0.083 / % possible all: 76.5
Reflection shell
*PLUS
% possible obs: 76.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.281 --RANDOM
Rwork0.182 ---
obs0.182 20524 86.1 %-
Displacement parametersBiso mean: 26.3 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 118 181 3323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.13
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3083 94 0.117 %
Rwork0.2793 802 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARACSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPF19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.07
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Rfactor obs: 0.2793

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