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- PDB-5eu7: Crystal structure of HIV-1 integrase catalytic core in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5eu7
TitleCrystal structure of HIV-1 integrase catalytic core in complex with Fab
Components
  • FAB Heavy Chain
  • FAB light chain
  • Integrase
KeywordsVIRAL PROTEIN / Integrase / FAB / HIV
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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Assembly Of The HIV Virion / 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 / 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 / peptidase activity / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsGalilee, M. / Griner, S.L. / Stroud, R.M. / Alian, A.
CitationJournal: Structure / Year: 2016
Title: The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical.
Authors: Galilee, M. / Britan-Rosich, E. / Griner, S.L. / Uysal, S. / Baumgartel, V. / Lamb, D.C. / Kossiakoff, A.A. / Kotler, M. / Stroud, R.M. / Marx, A. / Alian, A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
E: FAB Heavy Chain
F: FAB Heavy Chain
D: FAB light chain
C: FAB light chain


Theoretical massNumber of molelcules
Total (without water)129,8236
Polymers129,8236
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.489, 87.650, 96.339
Angle α, β, γ (deg.)90.00, 95.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A57 - 209
2113B57 - 209
1123C1 - 214
2123D1 - 214
1133E1 - 231
2133F1 - 231

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.849031, 0.526542, -0.043581), (0.526353, 0.835801, -0.156167), (-0.045804, -0.15553, -0.986769)48.84688, -6.37717, 89.60323

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Components

#1: Protein Integrase / Pr160Gag-Pol


Mass: 16710.076 Da / Num. of mol.: 2 / Fragment: Catalytic Core Domain, UNP residues 36-188 / Mutation: F185K, W131D
Source method: isolated from a genetically manipulated source
Details: Integrase Central Core Domain / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Antibody FAB Heavy Chain


Mass: 24927.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody FAB light chain


Mass: 23273.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 100mM BisTrisPropane pH 7.0

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.64→95.84 Å / Num. obs: 42891 / % possible obs: 98.7 % / Redundancy: 7.53 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.54
Reflection shellResolution: 2.64→2.729 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 5.92 / % possible all: 92.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EX4 and 1FVD

1ex4

1fvd


Resolution: 2.64→95.84 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.094 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 1.18 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23317 2014 5 %RANDOM
Rwork0.18136 ---
obs0.18401 38035 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.309 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å2-0 Å2-0.59 Å2
2---0.52 Å20 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.64→95.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8883 0 0 235 9118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0199089
X-RAY DIFFRACTIONr_bond_other_d0.0060.028377
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.94612338
X-RAY DIFFRACTIONr_angle_other_deg2.761319373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67151156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25924.373359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.286151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9991532
X-RAY DIFFRACTIONr_chiral_restr0.0920.21385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210268
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022036
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0654.0344654
X-RAY DIFFRACTIONr_mcbond_other3.0654.0334653
X-RAY DIFFRACTIONr_mcangle_it4.7536.0315800
X-RAY DIFFRACTIONr_mcangle_other4.7536.0325801
X-RAY DIFFRACTIONr_scbond_it4.0044.4114435
X-RAY DIFFRACTIONr_scbond_other4.0034.4114436
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3226.4226539
X-RAY DIFFRACTIONr_long_range_B_refined9.25837.99636676
X-RAY DIFFRACTIONr_long_range_B_other9.25837.99736677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1355LOOSE POSITIONAL0.395
1A840TIGHT THERMAL3.810.5
1A1355LOOSE THERMAL5.5610
2C1886LOOSE POSITIONAL0.415
2C1244TIGHT THERMAL5.240.5
2C1886LOOSE THERMAL6.4610
3E1953LOOSE POSITIONAL0.385
3E1322TIGHT THERMAL3.740.5
3E1953LOOSE THERMAL5.3210
LS refinement shellResolution: 2.635→2.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 131 -
Rwork0.263 2578 -
obs--90.39 %

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