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- PDB-4ewr: X-ray structure of WDR5-SETd1a Win motif peptide binary complex -

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Basic information

Entry
Database: PDB / ID: 4ewr
TitleX-ray structure of WDR5-SETd1a Win motif peptide binary complex
Components
  • Histone-lysine N-methyltransferase SETD1A
  • WD repeat-containing protein 5
KeywordsTranscription/Transferase / WD40 / Win motif / beta propeller / 3-10 helix / lysine methyltransferase / SETd1a / RbBP5 / MLL1 / Ash2L / core complex / Histone / Transcription-Transferase complex
Function / homology
Function and homology information


regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / regulation of hematopoietic stem cell differentiation / ATAC complex / NSL complex ...regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / regulation of hematopoietic stem cell differentiation / 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 / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / brain development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / beta-catenin binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / methylation / regulation of cell cycle / nuclear speck / DNA damage response / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Set1A, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Histone-lysine N-methyltransferase Set1-like / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...Set1A, RNA recognition motif / Histone-lysine N-methyltransferase SETD1A / COMPASS complex Set1 subunit, N-SET domain / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / Histone-lysine N-methyltransferase Set1-like / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / G-protein beta WD-40 repeat / Nucleotide-binding alpha-beta plait domain superfamily / 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 / Mainly Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETD1A / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.503 Å
AuthorsDharmarajan, V. / Lee, J.-H. / Patel, A. / Skalnik, D.G. / Cosgrove, M.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for WDR5 interaction (Win) motif recognition in human SET1 family histone methyltransferases.
Authors: Dharmarajan, V. / Lee, J.H. / Patel, A. / Skalnik, D.G. / Cosgrove, M.S.
History
DepositionApr 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: 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 1.3Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
C: Histone-lysine N-methyltransferase SETD1A


Theoretical massNumber of molelcules
Total (without water)35,8882
Polymers35,8882
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.494, 98.659, 80.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 34303.914 Da / Num. of mol.: 1 / Fragment: UNP residues 23-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIG3, WDR5 / Plasmid: pHIS paralell / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P61964
#2: Protein/peptide Histone-lysine N-methyltransferase SETD1A / Lysine N-methyltransferase 2F / SET domain-containing protein 1A / hSET1A / Set1/Ash2 histone ...Lysine N-methyltransferase 2F / SET domain-containing protein 1A / hSET1A / Set1/Ash2 histone methyltransferase complex subunit SET1


Mass: 1583.615 Da / Num. of mol.: 1 / Fragment: UNP residues 1488-1501 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O15047, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 7.6
Details: PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionRedundancy: 13.6 % / Av σ(I) over netI: 37.12 / Number: 673835 / Rmerge(I) obs: 0.1 / Χ2: 1.86 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 49713 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.235099.610.0442.68314.2
2.563.2310010.0732.66814
2.242.5610010.1022.32314.4
2.042.2410010.1232.09114.4
1.892.0410010.1631.84514.5
1.781.8999.910.2391.5214.5
1.691.7899.710.3461.37214.3
1.621.6999.610.4341.24513.6
1.551.6299.310.5341.18412.1
1.51.5598.910.6341.1889.5
ReflectionResolution: 1.5→50 Å / Num. obs: 49713 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.5-1.559.50.634198.9
1.55-1.6212.10.534199.3
1.62-1.6913.60.434199.6
1.69-1.7814.30.346199.7
1.78-1.8914.50.239199.9
1.89-2.0414.50.1631100
2.04-2.2414.40.1231100
2.24-2.5614.40.1021100
2.56-3.23140.0731100
3.23-5014.20.044199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.503→24.665 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.17 / σ(F): 1.34 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 2518 5.07 %
Rwork0.1728 --
obs0.1741 49670 99.65 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.803 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.267 Å20 Å2-0 Å2
2--3.6887 Å20 Å2
3----3.9558 Å2
Refinement stepCycle: LAST / Resolution: 1.503→24.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 0 322 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062482
X-RAY DIFFRACTIONf_angle_d1.1623365
X-RAY DIFFRACTIONf_dihedral_angle_d11.954877
X-RAY DIFFRACTIONf_chiral_restr0.08379
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.503-1.53180.33631380.25842531X-RAY DIFFRACTION98
1.5318-1.5630.25461400.23012559X-RAY DIFFRACTION99
1.563-1.5970.24561420.20472585X-RAY DIFFRACTION99
1.597-1.63420.21521420.19612569X-RAY DIFFRACTION99
1.6342-1.6750.23461380.18422610X-RAY DIFFRACTION100
1.675-1.72030.24781310.182587X-RAY DIFFRACTION100
1.7203-1.77090.20351620.17062582X-RAY DIFFRACTION100
1.7709-1.8280.17241320.16822605X-RAY DIFFRACTION100
1.828-1.89330.15581610.16082593X-RAY DIFFRACTION100
1.8933-1.96910.16581400.16192626X-RAY DIFFRACTION100
1.9691-2.05870.2081550.16862593X-RAY DIFFRACTION100
2.0587-2.16720.20721220.17052648X-RAY DIFFRACTION100
2.1672-2.30290.19041520.17052606X-RAY DIFFRACTION100
2.3029-2.48050.21191200.16912657X-RAY DIFFRACTION100
2.4805-2.72990.2031380.17942657X-RAY DIFFRACTION100
2.7299-3.12420.22361370.17892660X-RAY DIFFRACTION100
3.1242-3.93360.17311250.1562708X-RAY DIFFRACTION100
3.9336-24.66810.16921430.16322776X-RAY DIFFRACTION100

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