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- PDB-1a8k: CRYSTALLOGRAPHIC ANALYSIS OF HUMAN IMMUNODEFICIENCY VIRUS 1 PROTE... -

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Basic information

Entry
Database: PDB / ID: 1a8k
TitleCRYSTALLOGRAPHIC ANALYSIS OF HUMAN IMMUNODEFICIENCY VIRUS 1 PROTEASE WITH AN ANALOG OF THE CONSERVED CA-P2 SUBSTRATE: INTERACTIONS WITH FREQUENTLY OCCURRING GLUTAMIC ACID RESIDUE AT P2' POSITION OF SUBSTRATES
ComponentsHIV PROTEASEHIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HUMAN IMMUNODEFICIENCY VIRUS PROTEASE / PROTON-MEDIATED INTERACTION / VIRAL MATURATION / HYDROLASE-HYDROLASE INHIBITOR 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 genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
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
AuthorsWeber, I.T. / Wu, J. / Adomat, J. / Harrison, R.W. / Kimmel, A.R. / Wondrak, E.M. / Louis, J.M.
CitationJournal: Eur.J.Biochem. / Year: 1997
Title: Crystallographic analysis of human immunodeficiency virus 1 protease with an analog of the conserved CA-p2 substrate -- interactions with frequently occurring glutamic acid residue at P2' position of substrates.
Authors: Weber, I.T. / Wu, J. / Adomat, J. / Harrison, R.W. / Kimmel, A.R. / Wondrak, E.M. / Louis, J.M.
History
DepositionMar 27, 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 / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,8856
Polymers43,2194
Non-polymers1,6662
Water2,864159
1
A: HIV PROTEASE
B: HIV PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4433
Polymers21,6102
Non-polymers8331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-30 kcal/mol
Surface area9170 Å2
MethodPISA
2
D: HIV PROTEASE
E: HIV PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4433
Polymers21,6102
Non-polymers8331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-33 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.600, 52.200, 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
HIV PROTEASE / HIV-1 protease


Mass: 10804.808 Da / Num. of mol.: 4 / Mutation: Q7K, L33I, L63I
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 / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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 HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, WHILE ...MUTATIONS Q7K, L33I, L63I 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: 2.14 Å3/Da / Density % sol: 42.41 %
Description: THE DATA WAS COLLECTED ON AN R-AXIS IMAGING PLATE DETECTOR MOUNTED ON AN RU200 RIGAKU ROTATING ANODE X-RAY GENERATOR THAT WAS OPERATED AT 50 KV AND 100 MA WITH A 0.5-MM COLLIMATOR. EACH ...Description: THE DATA WAS COLLECTED ON AN R-AXIS IMAGING PLATE DETECTOR MOUNTED ON AN RU200 RIGAKU ROTATING ANODE X-RAY GENERATOR THAT WAS OPERATED AT 50 KV AND 100 MA WITH A 0.5-MM COLLIMATOR. EACH OSCILLATION FRAME WAS EXPOSED FOR 45 MIN. AT ROOM TEMPERATURE WITH 3.0 OSCILLATIONS. THE DISTANCE TO THE DETECTOR PLATE WAS SET AT 100 MM.
Crystal growpH: 4.7 / Details: pH 4.7
Crystal grow
*PLUS
Method: vapor diffusion / Details: macroseeding with 40-41% ammonium sulfate
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 %dimethyl sulfoxide1reservoir
944-45 %satammonium sulfate1reservoir
4inhibitor1dropfivefold 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: Mar 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: 10077 / % possible obs: 80.8 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.1009 / Rsym value: 0.19 / Net I/σ(I): 2
Reflection shellResolution: 2.06→2.25 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.092 / % possible all: 46.6
Reflection shell
*PLUS
% possible obs: 46.6 % / Num. unique obs: 3345

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7HVP

7hvp


Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.319 1211 7.9 %RANDOM
Rwork0.174 ---
obs0.174 -65.7 %-
Displacement parametersBiso mean: 0.26 Å2 /
Baniso -2Baniso -3
1-0 Å20 Å2
2--0 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 118 159 3309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.22
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 / Total num. of bins used: 438
RfactorNum. reflection% reflection
Rfree0.4209 31 7.1 %
Rwork0.3148 407 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3NLE.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.08
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.22

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