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- PDB-6trj: LEDGF/p75 IBD dimer -

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Basic information

Entry
Database: PDB / ID: 6trj
TitleLEDGF/p75 IBD dimer
ComponentsPC4 and SFRS1-interacting protein
KeywordsPROTEIN BINDING / protein-protein interaction / transcription factor
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 / euchromatin / response to heat / DNA-binding transcription factor binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / chromatin binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.3 Å
AuthorsKugler, M. / Brynda, J.
CitationJournal: Structure
Title: Fine-tuning of the LEDGF/p75 interaction network by dimerization
Authors: Lux, V. / Brouns, T. / Cermakova, K. / Srb, P. / Fabry, M. / Madlikova, M. / Horejsi, M. / Kugler, M. / Brynda, J. / Novak, P. / DeRijck, J. / Christ, F. / Debyser, Z. / Veverka, V.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PC4 and SFRS1-interacting protein


Theoretical massNumber of molelcules
Total (without water)10,5191
Polymers10,5191
Non-polymers00
Water2,054114
1
A: PC4 and SFRS1-interacting protein

A: PC4 and SFRS1-interacting protein


Theoretical massNumber of molelcules
Total (without water)21,0392
Polymers21,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4410 Å2
ΔGint-50 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.748, 58.748, 48.232
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-107-

HOH

21A-214-

HOH

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Components

#1: Protein PC4 and SFRS1-interacting protein / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52


Mass: 10519.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: O75475
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1 M Tris (base); BICINE pH 8.5; 20% v/v Glycerol; 10% w/v PEG 4000 ...Details: 0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1 M Tris (base); BICINE pH 8.5; 20% v/v Glycerol; 10% w/v PEG 4000 (Morpheus Molecular Dimensions condition H11)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.3→50.88 Å / Num. obs: 22048 / % possible obs: 91.8 % / Redundancy: 5.467 % / Biso Wilson estimate: 21.766 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Χ2: 1.02 / Net I/σ(I): 17.65 / Num. measured all: 120531
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.382.6150.8270.966668383425500.4981.00166.5
1.38-1.473.6930.571.9111756359531830.7310.66488.5
1.47-1.594.1420.294.1313064336731540.9230.33293.7
1.59-1.744.3830.1766.6713264309130260.9750.297.9
1.74-1.954.960.10811.9914115284628460.9920.121100
1.95-2.256.520.05827.4216190248324830.9980.063100
2.25-2.759.5720.04143.720464213921380.9990.043100
2.75-3.8810.0070.03355.7616852168416840.9990.035100
3.88-50.888.2910.03358.8181589869840.9990.03599.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.3→50.88 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.872 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0455 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 1089 4.9 %RANDOM
Rwork0.1373 ---
obs0.1393 20959 91.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.12 Å2 / Biso mean: 22.167 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.3→50.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms684 0 0 115 799
Biso mean---33.38 -
Num. residues----85
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019712
X-RAY DIFFRACTIONr_bond_other_d0.0010.02723
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.969958
X-RAY DIFFRACTIONr_angle_other_deg1.09831665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.862591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0962532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58415157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.178155
X-RAY DIFFRACTIONr_chiral_restr0.080.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02155
X-RAY DIFFRACTIONr_rigid_bond_restr3.9513709
X-RAY DIFFRACTIONr_sphericity_free25.953516
X-RAY DIFFRACTIONr_sphericity_bonded13.4585769
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 32 -
Rwork0.332 792 -
all-824 -
obs--46.79 %

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