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- PDB-4u7q: Structure of wild-type HIV protease in complex with photosensitiv... -

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Basic information

Entry
Database: PDB / ID: 4u7q
TitleStructure of wild-type HIV protease in complex with photosensitive inhibitor PDI-6
ComponentsV-1 protease
KeywordsHYDROLASE / HIV-1 / viral protease / aspartic protease / inhibition
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 / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / 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 / symbiont-mediated suppression of host gene expression / 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 / peptidase activity / 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 / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / 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
Chem-3EM / Gag-Pol polyprotein / V-1 protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsPachl, P. / Rezacova, P. / Schimer, J.
Funding support Czech Republic, Germany, 3items
OrganizationGrant numberCountry
Ministry of Education of the CzechRepublicP208-12-G016 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLO 1302 Czech Republic
German Research FoundationMU885/5-1 Germany
CitationJournal: Nat Commun / Year: 2015
Title: Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor.
Authors: Schimer, J. / Pavova, M. / Anders, M. / Pachl, P. / Sacha, P. / Cigler, P. / Weber, J. / Majer, P. / Rezacova, P. / Krausslich, H.G. / Muller, B. / Konvalinka, J.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / software / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-1 protease
B: V-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4083
Polymers21,6102
Non-polymers7981
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-22 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.841, 62.841, 80.486
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 99 / Label seq-ID: 1 - 99

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a dimer. There is one biological unit in the asymetric unit

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Components

#1: Protein V-1 protease


Mass: 10804.808 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: ORF / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL / References: UniProt: Q9Q2G4, UniProt: P04585*PLUS
#2: Chemical ChemComp-3EM / N~2~-({[7-(diethylamino)-2-oxo-2H-chromen-4-yl]methoxy}carbonyl)-N-[(2S,4S,5S)-4-hydroxy-1,6-diphenyl-5-{[(1,3-thiazol-5-ylmethoxy)carbonyl]amino}hexan-2-yl]-L-valinamide


Mass: 797.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H51N5O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 200mM LiCl, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.61→10 Å / Num. obs: 23062 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 32.025 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.045 / Χ2: 0.938 / Net I/σ(I): 20.76 / Num. measured all: 116704
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.61-1.710.7730.6352.5718612371437070.71199.8
1.71-1.820.9190.3584.5217685349434930.4100
1.82-1.970.980.1758.8816393326032340.19699.2
1.97-2.160.9940.0916.2715381302130210.1100
2.16-2.410.9970.05923.613794272127000.06699.2
2.41-2.780.9990.04132.6512200238523850.046100
2.78-3.410.9990.0345.9110372204820480.033100
3.41-4.80.9990.02556.457983158815860.02799.9
4.80.9990.02356.6542848928880.02699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation44.93 Å3 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
MOLREPphasing
REFMAC5.8.0071refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDW

3ndw


Resolution: 1.7→10 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.3235 / WRfactor Rwork: 0.2768 / FOM work R set: 0.6658 / SU B: 5.178 / SU ML: 0.17 / SU R Cruickshank DPI: 0.1808 / SU Rfree: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3262 978 5 %RANDOM
Rwork0.2749 18654 --
obs0.2775 19632 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.64 Å2 / Biso mean: 34.869 Å2 / Biso min: 13.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 114 93 1686
Biso mean--25.11 35.47 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021645
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211671
X-RAY DIFFRACTIONr_angle_refined_deg2.1912.0572239
X-RAY DIFFRACTIONr_angle_other_deg1.4013.023839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11825.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83615272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.786155
X-RAY DIFFRACTIONr_chiral_restr0.1220.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02337
X-RAY DIFFRACTIONr_mcbond_it3.2443.456796
X-RAY DIFFRACTIONr_mcbond_other3.2333.454795
X-RAY DIFFRACTIONr_mcangle_it4.5765.179993
Refine LS restraints NCS

Ens-ID: 1 / Number: 5510 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 61 -
Rwork0.346 1253 -
all-1314 -
obs--92.93 %

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