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- PDB-2r8n: Structural Analysis of the Unbound Form of HIV-1 Subtype C Protease -

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Basic information

Entry
Database: PDB / ID: 2r8n
TitleStructural Analysis of the Unbound Form of HIV-1 Subtype C Protease
ComponentsPol protein
KeywordsHYDROLASE / HIV-1 subtype C / Aspartyl protease / Multifunctional enzyme / Nucleotidyltransferase / Protease / RNA-directed DNA polymerase / Transferase
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / 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 / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane / metal ion binding
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 / 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. / Ribonuclease H superfamily / 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
Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsComan, R.M. / Robbins, A.H. / McKenna, R. / Dunn, B.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: High-resolution structure of unbound human immunodeficiency virus 1 subtype C protease: implications of flap dynamics and drug resistance.
Authors: Coman, R.M. / Robbins, A.H. / Goodenow, M.M. / Dunn, B.M. / McKenna, R.
History
DepositionSep 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.4Jul 28, 2021Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id ..._refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999The authors state that the PR clone used in this study does not harbor a frequent polymorphism ...The authors state that the PR clone used in this study does not harbor a frequent polymorphism found in subtype C PRs:R41K. It is one of the residues that appear to be involved in preserving or augmenting the catalytic efficiency of the subtype C PR and enhancing the viral fitness when compared to subtype B viruses.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9363
Polymers10,7521
Non-polymers1842
Water2,990166
1
A: Pol protein
hetero molecules

A: Pol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8726
Polymers21,5042
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.711, 46.711, 100.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-303-

HOH

31A-304-

HOH

41A-436-

HOH

DetailsThe biological unit is a homodimer. There is one half of the biological unit in the asymmetric unit (chain A).

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Components

#1: Protein Pol protein


Mass: 10751.787 Da / Num. of mol.: 1 / Fragment: HIV-1 protease subtype C, UNP residues 1-99 / Mutation: Q7K, L33I, L63I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: subtype C / Gene: pol / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star pLysS / References: UniProt: Q8ALR4, UniProt: O12158*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30 mM citric acid, 1 M NaCl, TritonX-100, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 35611 / Num. obs: 33850 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Χ2: 0.858 / Net I/σ(I): 14
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3349 / Rsym value: 0.273 / Χ2: 0.713 / % possible all: 95.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SHELXLrefinement
SCALEPACKdata scaling
CNSrefinement
SHELXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→23.5 Å / Cross valid method: R-free / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1667 -random
Rwork0.141 ---
obs0.141 33850 95.1 %-
all-35611 --
Displacement parametersBiso mean: 19.994 Å2
Refinement stepCycle: LAST / Resolution: 1.2→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 12 166 932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.04

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