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- PDB-8x3r: Crystal structure of human WDR5 in complex with WDR5 -

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Basic information

Entry
Database: PDB / ID: 8x3r
TitleCrystal structure of human WDR5 in complex with WDR5
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION / epigenetics / cell proliferation
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLiu, Y. / Huang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271309 China
CitationJournal: Cell Death Dis / Year: 2024
Title: The NTE domain of PTEN alpha / beta promotes cancer progression by interacting with WDR5 via its SSSRRSS motif.
Authors: Huang, X. / Zhang, C. / Shang, X. / Chen, Y. / Xiao, Q. / Wei, Z. / Wang, G. / Zhen, X. / Xu, G. / Min, J. / Shen, S. / Liu, Y.
History
DepositionNov 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5


Theoretical massNumber of molelcules
Total (without water)73,2712
Polymers73,2712
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-5 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.560, 52.660, 123.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WD repeat-containing protein 5


Mass: 36635.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium formate dihydrate, 15% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→24.21 Å / Num. obs: 30780 / % possible obs: 96.9 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.9
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 1719 / CC1/2: 0.674

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→24.21 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 2002 6.51 %
Rwork0.1647 --
obs0.1674 30753 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 0 181 2596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d7.681324
X-RAY DIFFRACTIONf_chiral_restr0.093379
X-RAY DIFFRACTIONf_plane_restr0.01417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.31371460.25322002X-RAY DIFFRACTION96
1.8-1.850.2721330.21252062X-RAY DIFFRACTION98
1.85-1.910.23261560.1942074X-RAY DIFFRACTION99
1.91-1.970.24111410.17242103X-RAY DIFFRACTION99
1.97-2.040.24981360.17462109X-RAY DIFFRACTION98
2.04-2.120.20561560.16622046X-RAY DIFFRACTION97
2.12-2.220.20621340.15792064X-RAY DIFFRACTION98
2.22-2.330.21541490.16012048X-RAY DIFFRACTION97
2.33-2.480.22151380.16292068X-RAY DIFFRACTION96
2.48-2.670.2271500.16022030X-RAY DIFFRACTION95
2.67-2.940.17721350.15612063X-RAY DIFFRACTION96
2.94-3.360.18961450.14852009X-RAY DIFFRACTION93
3.36-4.230.18171360.14712031X-RAY DIFFRACTION92
4.24-24.210.18161470.17332042X-RAY DIFFRACTION89

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