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- PDB-2nph: Crystal structure of HIV1 protease in situ product complex -

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Basic information

Entry
Database: PDB / ID: 2nph
TitleCrystal structure of HIV1 protease in situ product complex
Components
  • PROTEASE RETROPEPSIN
  • pentapeptide fragment
  • tetrapeptide fragment
KeywordsHYDROLASE / anti-parallel beta sheet
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 / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase 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 / identical protein 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 / 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
Gag-Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHosur, M.V. / Das, A. / Prashar, V.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates
Authors: Das, A. / Prashar, V. / Mahale, S. / Serre, L. / Ferrer, J.-L. / Hosur, M.V.
#1: Journal: Biochem.J. / Year: 2005
Title: Observation of a tetrahedral reaction intermediate in HIV-1 protease substrate complex
Authors: Kumar, M. / Prashar, V. / Mahale, S. / Hosur, M.V.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Rapid screening for HIV-1 protease inhibitor leads through X-ray diffraction
Authors: Pillai, B. / Bhat, S.V. / Kannan, K.K. / Hosur, M.V.
#3: Journal: Proteins / Year: 2001
Title: 1.9A X-ray study shows closed flap conformation in crystals of tethered HIV-1 PR
Authors: Pillai, B. / Kannan, K.K. / Hosur, M.V.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Effects of remote mutation on the autolysis of HIV-1 PR: X-ray and NMR investigations
Authors: Kumar, M. / Kannan, K.K. / Hosur, M.V. / Bhavesh, N.S. / Chatterjee, A. / Mittal, R. / Hosur, R.V.
History
DepositionOct 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 1.6Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
S: tetrapeptide fragment
T: pentapeptide fragment


Theoretical massNumber of molelcules
Total (without water)22,6264
Polymers22,6264
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-26 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.030, 62.030, 81.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsThe functional dimer is in the asymmetric unit.

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Components

#1: Protein PROTEASE RETROPEPSIN / E.C.3.4.23.16 / HIV-1 PROTEASE


Mass: 10817.782 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Observation of a Low Barrier Hydrogen Bond between catalytic aspartates
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: pol / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q72874, UniProt: P04585*PLUS, HIV-1 retropepsin
#2: Protein/peptide tetrapeptide fragment


Mass: 466.484 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein/peptide pentapeptide fragment


Mass: 523.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Ammonium Sulfate precipitant, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97945 Å
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.65→32.53 Å / Num. all: 20957 / Num. obs: 20326 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.53 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 10.16

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345CCD 165data collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→32.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.895 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1069 5 %RANDOM
Rwork0.214 ---
all0.216 20957 --
obs0.216 20326 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 0 156 1741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221611
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9892183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.93824.82858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52615290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.582158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021163
X-RAY DIFFRACTIONr_nbd_refined0.2530.3823
X-RAY DIFFRACTIONr_nbtor_refined0.3310.51113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2830.7190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.382
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.760.738
X-RAY DIFFRACTIONr_mcbond_it1.161.51041
X-RAY DIFFRACTIONr_mcangle_it1.94521652
X-RAY DIFFRACTIONr_scbond_it2.9413634
X-RAY DIFFRACTIONr_scangle_it4.8924.5531
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 79 -
Rwork0.302 1501 -
obs-1580 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.80831.51432.27141.12091.30231.85690.0014-0.0063-0.0667-0.01130.0283-0.03730.00120.0131-0.0297-0.0561-0.0396-0.0121-0.0027-0.0068-0.0374-11.359519.757727.6314
2000000000000000000000000
310.583811.4536-14.31412.4109-15.74323.3387-0.26950.0426-1.3048-0.28960.207-1.14240.18410.44740.0625-0.0009-0.0007-0.00070.0004-0.0019-0.0018-8.11514.949826.855
4000000000000000000000000
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 991 - 99
21BB1001 - 10991 - 99
33SC1 - 41 - 4
43TD5 - 91 - 5

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