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- PDB-4fu6: Crystal structure of the PSIP1 PWWP domain -

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Basic information

Entry
Database: PDB / ID: 4fu6
TitleCrystal structure of the PSIP1 PWWP domain
ComponentsPC4 and SFRS1-interacting protein
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / 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 / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / 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 / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsQin, S. / Tempel, W. / Xu, C. / Wu, H. / Dong, A. / Cerovina, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Trends Biochem.Sci. / Year: 2014
Title: Structure and function of the nucleosome-binding PWWP domain.
Authors: Qin, S. / Min, J.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Aug 4, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,89910
Polymers17,5181
Non-polymers3809
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.960, 45.960, 156.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-303-

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: 17518.379 Da / Num. of mol.: 1 / Fragment: UNP residues 1-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75475
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCALCULATED VALUES FOR MATTHEWS COEFFICIENT AND SOLVENT CONTENT(2.35/47.77) ARE BASED ON THE ENTIRE ...CALCULATED VALUES FOR MATTHEWS COEFFICIENT AND SOLVENT CONTENT(2.35/47.77) ARE BASED ON THE ENTIRE SEQUENCE OF THE CONSTRUCT. AUTHOR STATES THAT THE ACTUAL SEQUENCE MAY BE SHORTER DUE TO PROTEOLYTIC ACTIVITY.

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: The protein sample was treated with V8 protease. 2.5M ammonium sulfate, 0.1M TRIS, pH 8.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97944 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 10584 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.081 / Χ2: 1.763 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1411.40.9814821.2411100
2.14-2.18120.8435321.251100
2.18-2.2212.90.8154951.3281100
2.22-2.2613.20.7595101.4041100
2.26-2.3113.70.5775201.3121100
2.31-2.37140.4795021.3181100
2.37-2.42140.4445351.2881100
2.42-2.4914.10.3815001.4211100
2.49-2.56140.2845391.4051100
2.56-2.6514.20.2695031.4211100
2.65-2.74140.2035241.5561100
2.74-2.8514.20.1535241.5251100
2.85-2.9813.90.1245251.5391100
2.98-3.14140.15291.8591100
3.14-3.3313.70.0855352.3711100
3.33-3.5913.50.0715292.9681100
3.59-3.9513.40.065402.983199.8
3.95-4.5213.30.0485492.698199.5
4.52-5.712.90.0425702.211100
5.7-5011.40.0366411.9021100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3QBY

3qby


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.198 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.875 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. the program COOT and the molprobity server were also used. CAVEAT: the C-terminal direction of the protein main ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. the program COOT and the molprobity server were also used. CAVEAT: the C-terminal direction of the protein main chain at LYS-91 is not resolved by electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 497 4.742 %RANDOM
Rwork0.1999 ---
obs0.201 10481 99.971 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 107.07 Å2 / Biso mean: 46.012 Å2 / Biso min: 27.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.119 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 26 30 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02797
X-RAY DIFFRACTIONr_bond_other_d0.0020.02699
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9711081
X-RAY DIFFRACTIONr_angle_other_deg0.80131617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.521593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06123.78437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55715115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.306153
X-RAY DIFFRACTIONr_chiral_restr0.0890.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1540.267270.3170673499.864
2.154-2.2130.388360.26169172899.863
2.213-2.2770.253390.239674713100
2.277-2.3470.282350.214656691100
2.347-2.4240.279370.2649686100
2.424-2.5080.31250.201623648100
2.508-2.6030.195340.211593627100
2.603-2.7090.238360.202600636100
2.709-2.8280.245420.193518560100
2.828-2.9660.257290.209539568100
2.966-3.1250.211200.209515535100
3.125-3.3140.24180.212505523100
3.314-3.5410.291110.188473484100
3.541-3.8220.2190.171439458100
3.822-4.1830.18190.16640042099.762
4.183-4.670.15220.139373395100
4.67-5.380.205190.179325344100
5.38-6.560.301160.236296312100
6.56-9.1550.20990.218237246100
9.155-400.42840.313160164100
Refinement TLS params.Method: refined / Origin x: 7.1569 Å / Origin y: 5.8533 Å / Origin z: 52.1674 Å
111213212223313233
T0.2711 Å20.0004 Å2-0.0854 Å2-0.0044 Å2-0.0074 Å2--0.1459 Å2
L3.1642 °20.8377 °21.5709 °2-5.6695 °23.7399 °2--7.432 °2
S-0.0651 Å °0.0061 Å °0.093 Å °0.3604 Å °-0.1062 Å °0.026 Å °-0.18 Å °-0.1098 Å °0.1713 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 91
2X-RAY DIFFRACTION1A201 - 209
3X-RAY DIFFRACTION1A301 - 330

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