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- PDB-3avc: Crystal structures of novel allosteric peptide inhibitors of HIV ... -

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Basic information

Entry
Database: PDB / ID: 3avc
TitleCrystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site
Components
  • Integrase
  • LEDGF peptide
KeywordsRECOMBINATION/INHIBITOR / protein-protein interactions / HIV / RECOMBINATION-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 / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / 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 ...Ribonuclease H-like superfamily/Ribonuclease H / 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 / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsPeat, T.S. / Deadman, J.J. / Newman, J. / Rhodes, D.I.
CitationJournal: Chembiochem / Year: 2011
Title: Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site.
Authors: Rhodes, D.I. / Peat, T.S. / Vandegraaff, N. / Jeevarajah, D. / Newman, J. / Martyn, J. / Coates, J.A. / Ede, N.J. / Rea, P. / Deadman, J.J.
History
DepositionMar 2, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Mar 13, 2013Group: Other
Revision 1.3Jun 19, 2013Group: Database references
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
B: Integrase
D: LEDGF peptide
F: LEDGF peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,88916
Polymers41,9294
Non-polymers96012
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-24 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.945, 70.945, 66.995
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDF

#1: Protein Integrase / / IN


Mass: 20044.672 Da / Num. of mol.: 2 / Fragment: CCD domain (UNP RESIDUES 1197-1359) / Mutation: C56S, F139D, F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: NEW YORK-5 ISOLATE / Gene: gag-pol / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497
#2: Protein/peptide LEDGF peptide / lens epithelial derived growth factor


Mass: 919.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthsis / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 144 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K
PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.77→19.6 Å / Num. all: 36751 / Num. obs: 36751

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.6.0062refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→19.08 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.956 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 1861 5.1 %RANDOM
Rwork0.1576 ---
obs0.1596 36728 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.51 Å2 / Biso mean: 26.3681 Å2 / Biso min: 9.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å20 Å2
2--0.49 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.77→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 50 132 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222731
X-RAY DIFFRACTIONr_angle_refined_deg2.3071.9563745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92225.763118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47615490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.336158
X-RAY DIFFRACTIONr_chiral_restr0.2060.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212046
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 148 -
Rwork0.23 2568 -
all-2716 -
obs--100 %

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