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- PDB-2b4j: Structural basis for the recognition between HIV-1 integrase and ... -

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Basic information

Entry
Database: PDB / ID: 2b4j
TitleStructural basis for the recognition between HIV-1 integrase and LEDGF/p75
Components
  • Integrase (IN)
  • PC4 and SFRS1 interacting protein
Keywordsviral protein / recombination / HIV / integration / transcription
Function / homology
Function and homology information


supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin ...supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / euchromatin / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / response to heat / viral nucleocapsid / DNA-binding transcription factor binding / DNA recombination / response to oxidative stress / DNA-directed DNA polymerase / transcription coactivator activity / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / chromatin remodeling / symbiont entry into host cell / viral translational frameshifting / lipid binding / chromatin binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 / 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 / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / PC4 and SFRS1-interacting protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsCherepanov, P. / Ambrosio, A.L. / Rahman, S. / Ellenberger, T. / Engelman, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75
Authors: Cherepanov, P. / Ambrosio, A.L. / Rahman, S. / Ellenberger, T. / Engelman, A.
History
DepositionSep 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 1.5Aug 23, 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: Integrase (IN)
B: Integrase (IN)
C: PC4 and SFRS1 interacting protein
D: PC4 and SFRS1 interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,52410
Polymers58,9664
Non-polymers5586
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-41 kcal/mol
Surface area20310 Å2
MethodPISA
2
A: Integrase (IN)
B: Integrase (IN)
C: PC4 and SFRS1 interacting protein
D: PC4 and SFRS1 interacting protein
hetero molecules

A: Integrase (IN)
B: Integrase (IN)
C: PC4 and SFRS1 interacting protein
D: PC4 and SFRS1 interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,04820
Polymers117,9328
Non-polymers1,11712
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13640 Å2
ΔGint-78 kcal/mol
Surface area40360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.421, 60.593, 71.126
Angle α, β, γ (deg.)90.00, 109.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Integrase (IN)


Mass: 18194.760 Da / Num. of mol.: 2 / Fragment: HIV-1 integrase / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12497
#2: Protein PC4 and SFRS1 interacting protein / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine speckles ...Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine speckles 70 kDa protein / DFS 70 / CLL-associated antigen KW-7


Mass: 11288.199 Da / Num. of mol.: 2 / Fragment: LEDGF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, LEDGF / Plasmid: pCPGST75-81 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O75475
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 41.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 32648 / Num. obs: 32136 / % possible obs: 99.2 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 4.8 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.041 / Net I/σ(I): 18.9
Reflection shellResolution: 2.02→2.09 Å / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 3189 / Χ2: 1.007 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
CBASSdata collection
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1BIS (Integrase), 1Z9E (LEDGF)

1bis

1z9e


Resolution: 2.02→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.106 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1627 5.1 %RANDOM
Rwork0.181 ---
all0.183 30406 --
obs0.183 32113 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.386 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å21.3 Å2
2---0.38 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 34 220 3757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223584
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9524819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6925.033151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92215693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5381517
X-RAY DIFFRACTIONr_chiral_restr0.1320.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022553
X-RAY DIFFRACTIONr_nbd_refined0.2130.21687
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.212
X-RAY DIFFRACTIONr_mcbond_it0.9811.52295
X-RAY DIFFRACTIONr_mcangle_it1.623564
X-RAY DIFFRACTIONr_scbond_it2.77831487
X-RAY DIFFRACTIONr_scangle_it4.3614.51255
LS refinement shellResolution: 2.021→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 124 -
Rwork0.214 2223 -
all-2347 -
obs--98.32 %
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)
14.4292-0.5959-1.02571.74120.39171.82380.21540.34570.5314-0.0421-0.0868-0.0325-0.1932-0.0167-0.1286-0.06550.01260.0322-0.07160.0744-0.04690.8516-0.4794-21.0989
24.1647-0.3954-1.30460.9899-0.07161.6376-0.07120.3343-0.39680.0429-0.03660.23310.0937-0.25250.1078-0.0695-0.01030.0048-0.0585-0.0501-0.0106-13.536-12.9638-15.861
32.28330.56980.36085.12921.56672.5546-0.21460.16980.011-0.40250.17930.2188-0.0725-0.04910.0353-0.1407-0.0269-0.0106-0.1154-0.0025-0.1097-25.320519.5794-4.2029
42.6236-1.4640.5096.3798-3.1633.92440.13390.3782-0.1065-0.9928-0.126-0.04260.47440.0114-0.0079-0.03280.0122-0.0248-0.02830.0133-0.141618.1455-31.5844-18.216
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA56 - 20810 - 162
22BB57 - 20811 - 162
33CC345 - 4261 - 82
44DD345 - 4261 - 82

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