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- PDB-3l3u: Crystal structure of the HIV-1 integrase core domain to 1.4A -

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Basic information

Entry
Database: PDB / ID: 3l3u
TitleCrystal structure of the HIV-1 integrase core domain to 1.4A
ComponentsPOL polyprotein
KeywordsVIRAL PROTEIN / DNA INTEGRATION / AIDS / INTEGRASE / ENDONUCLEASE / POLYNUCLEOTIDYL TRANSFERASE / DNA BINDING
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / 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 / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsWielens, J. / Chalmers, D.K. / Scanlon, M.J. / Parker, M.W.
CitationJournal: Febs Lett. / Year: 2010
Title: Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site.
Authors: Wielens, J. / Headey, S.J. / Jeevarajah, D. / Rhodes, D.I. / Deadman, J. / Chalmers, D.K. / Scanlon, M.J. / Parker, M.W.
History
DepositionDec 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 10, 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 1.4Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: POL polyprotein
B: POL polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8935
Polymers35,6042
Non-polymers2883
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-17 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.550, 62.434, 81.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmultimer

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Components

#1: Protein POL polyprotein


Mass: 17802.174 Da / Num. of mol.: 2
Fragment: CATALYTIC CORE DOMAIN OF integrase, UNP residues 765-927
Mutation: C56S, W131D, W139D, F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL43 / Gene: pol / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q72498
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 41.92 % / Mosaicity: 0.19 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8M Ammonium sulfate, 0.15M sodium citrate, 5mM cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.90002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2006
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90002 Å / Relative weight: 1
ReflectionResolution: 1.4→34.015 Å / Num. all: 60131 / Num. obs: 60131 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 15.2
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 6.6 / Num. unique all: 8679 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.578 / Cor.coef. Fo:Fc: 0.216 / Cor.coef. Io to Ic: 0.199
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1exq

1exq


Resolution: 1.4→34.01 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.222 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.909 / SU B: 1.564 / SU ML: 0.029 / SU R Cruickshank DPI: 0.087 / SU Rfree: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.087 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3064 5.1 %RANDOM
Rwork0.204 ---
obs0.205 60063 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.21 Å2 / Biso mean: 11.97 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 15 334 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222571
X-RAY DIFFRACTIONr_bond_other_d0.0010.021689
X-RAY DIFFRACTIONr_angle_refined_deg2.0791.9493521
X-RAY DIFFRACTIONr_angle_other_deg1.10634184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88125102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44915459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6221510
X-RAY DIFFRACTIONr_chiral_restr0.1360.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02490
X-RAY DIFFRACTIONr_mcbond_it2.1981.51621
X-RAY DIFFRACTIONr_mcbond_other0.7341.5668
X-RAY DIFFRACTIONr_mcangle_it3.24622652
X-RAY DIFFRACTIONr_scbond_it5.0753950
X-RAY DIFFRACTIONr_scangle_it7.2274.5869
X-RAY DIFFRACTIONr_rigid_bond_restr2.13934260
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 224 -
Rwork0.264 4147 -
all-4371 -
obs--100 %

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