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- PDB-1kj4: SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION... -

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Basic information

Entry
Database: PDB / ID: 1kj4
TitleSUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES
Components
  • POL polyprotein
  • gag polyprotein
KeywordsHYDROLASE / MARIX-CAPSID / SUBSTRATE RECOGNITION
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 / 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 / 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 / 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 / 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
ACETATE ION / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchiffer, C.A.
CitationJournal: Structure / Year: 2002
Title: Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes.
Authors: Prabu-Jeyabalan, M. / Nalivaika, E. / Schiffer, C.A.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POL polyprotein
B: POL polyprotein
C: POL polyprotein
D: POL polyprotein
P: gag polyprotein
S: gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,23418
Polymers45,5266
Non-polymers70912
Water77543
1
A: POL polyprotein
B: POL polyprotein
P: gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,17610
Polymers22,7633
Non-polymers4137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-36 kcal/mol
Surface area9430 Å2
MethodPISA
2
C: POL polyprotein
D: POL polyprotein
S: gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0588
Polymers22,7633
Non-polymers2955
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-35 kcal/mol
Surface area9020 Å2
MethodPISA
3
A: POL polyprotein
B: POL polyprotein
C: POL polyprotein
D: POL polyprotein
P: gag polyprotein
S: gag polyprotein
hetero molecules

A: POL polyprotein
B: POL polyprotein
C: POL polyprotein
D: POL polyprotein
P: gag polyprotein
S: gag polyprotein
hetero molecules

A: POL polyprotein
B: POL polyprotein
C: POL polyprotein
D: POL polyprotein
P: gag polyprotein
S: gag polyprotein
hetero molecules

A: POL polyprotein
B: POL polyprotein
C: POL polyprotein
D: POL polyprotein
P: gag polyprotein
S: gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,93772
Polymers182,10324
Non-polymers2,83448
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area67200 Å2
ΔGint-359 kcal/mol
Surface area54860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.651, 93.808, 118.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsTHE ENTIRE BIOLOGICAL DIMER ALONG WITH THE SUBSTRATE PEPTIDE BOUND IN THE ACTIVE SITE ARE PROVIDED IN THIS COORDINATE FILE

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Components

#1: Protein
POL polyprotein


Mass: 10800.777 Da / Num. of mol.: 4 / Fragment: HIV-1 PROTEASE, RESIDUES 57-155 / Mutation: D25N,Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin
#2: Protein/peptide gag polyprotein


Mass: 1161.264 Da / Num. of mol.: 2 / Fragment: MATRIX-CAPSID SUBSTRATE PEPTIDE, RESIDUES 127-136 / Source method: obtained synthetically / References: UniProt: P20875
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Ammonium Sulphate, SODIUM PHOSPHATE, SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 26, 1999 / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→38.88 Å / Num. all: 12376 / Num. obs: 12376 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 4.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7A

1f7a


Resolution: 2.9→38.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 64173.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1031 10.4 %RANDOM
Rwork0.197 ---
obs0.197 12376 85.6 %-
all-12376 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.2161 Å2 / ksol: 0.341402 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å20 Å20 Å2
2--0.2 Å20 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 48 43 3170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ACE.PARAMACE.TOP

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