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- PDB-8wxv: Structure of WDR5 in complex with WIN motif containing SET1B -

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Basic information

Entry
Database: PDB / ID: 8wxv
TitleStructure of WDR5 in complex with WIN motif containing SET1B
Components
  • SET1B
  • WD repeat-containing protein 5
KeywordsNUCLEAR PROTEIN / WDR5 / SET1b / WIN motif / chromatin
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: 2.4 Å
AuthorsXu, L. / Yang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural studies of WDR5 in complex with MBD3C WIN motif reveal a unique binding mode.
Authors: Yang, Y. / Xu, L. / Zhang, S. / Yao, L. / Ding, Y. / Li, W. / Chen, X.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: SET1B
C: WD repeat-containing protein 5
D: SET1B


Theoretical massNumber of molelcules
Total (without water)71,4754
Polymers71,4754
Non-polymers00
Water3,963220
1
A: WD repeat-containing protein 5
B: SET1B


Theoretical massNumber of molelcules
Total (without water)35,7372
Polymers35,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area11370 Å2
MethodPISA
2
C: WD repeat-containing protein 5
D: SET1B


Theoretical massNumber of molelcules
Total (without water)35,7372
Polymers35,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-4 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.904, 61.499, 64.774
Angle α, β, γ (deg.)110.34, 91.27, 112.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34646.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Protein/peptide SET1B


Mass: 1091.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris, pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23662 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.47
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.292 / Num. unique obs: 1168

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→33.54 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2406 10.17 %
Rwork0.1676 --
obs0.1714 23652 97.78 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→33.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 0 220 4940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044834
X-RAY DIFFRACTIONf_angle_d0.8156557
X-RAY DIFFRACTIONf_dihedral_angle_d6.86638
X-RAY DIFFRACTIONf_chiral_restr0.057743
X-RAY DIFFRACTIONf_plane_restr0.005812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.26261410.21751227X-RAY DIFFRACTION94
2.45-2.50.28621360.20321195X-RAY DIFFRACTION97
2.5-2.560.28661570.20931255X-RAY DIFFRACTION97
2.56-2.620.28061420.19771223X-RAY DIFFRACTION98
2.62-2.690.23491390.18841257X-RAY DIFFRACTION97
2.69-2.770.21741390.18271258X-RAY DIFFRACTION97
2.77-2.860.23811410.17641208X-RAY DIFFRACTION97
2.86-2.960.2541400.18181280X-RAY DIFFRACTION98
2.96-3.080.21921510.18451248X-RAY DIFFRACTION98
3.08-3.220.23451340.17471252X-RAY DIFFRACTION98
3.22-3.390.22141240.17461278X-RAY DIFFRACTION99
3.39-3.610.18891630.16681266X-RAY DIFFRACTION98
3.61-3.880.24231150.17481257X-RAY DIFFRACTION99
3.88-4.270.17611210.13371296X-RAY DIFFRACTION99
4.27-4.890.14011460.12331245X-RAY DIFFRACTION99
4.89-6.150.16521710.14991246X-RAY DIFFRACTION98
6.16-33.540.15621460.16841255X-RAY DIFFRACTION99
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)
12.1037-0.71811.01462.8865-0.35032.3611-0.1308-0.26240.06950.10810.0465-0.1486-0.2811-0.04380.07860.16360.00250.02260.22260.02520.1579-14.717121.473715.2587
26.54052.76561.04436.591.78870.50150.1349-0.92350.14391.6178-0.3225-0.3886-0.19570.87040.18660.8493-0.0635-0.23091.08470.20280.4864-19.688415.074327.078
31.7320.31730.3143.4184-0.63633.3224-0.0280.07-0.1159-0.2020.12080.16170.46-0.2277-0.090.1863-0.0213-0.02290.25760.04660.186-36.378724.4307-16.5127
47.8807-3.8447-1.67557.79252.78861.0130.41010.3816-0.0473-0.3842-0.5397-0.32650.53930.10380.12861.1353-0.1587-0.07850.76450.33760.6738-41.283630.0722-28.6372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 32 through 334)
2X-RAY DIFFRACTION2(chain 'B' and resid 1745 through 1752)
3X-RAY DIFFRACTION3(chain 'C' and resid 32 through 334)
4X-RAY DIFFRACTION4(chain 'D' and resid 1745 through 1752)

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