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- PDB-3emh: Structural basis of WDR5-MLL interaction -

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Basic information

Entry
Database: PDB / ID: 3emh
TitleStructural basis of WDR5-MLL interaction
Components
  • Mixed-lineage leukemia protein 1
  • WD repeat-containing protein 5
KeywordsGENE REGULATION / Chromatin / Histone / WD40 repeat / Nucleus / Phosphoprotein / WD repeat / Zinc-finger
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / definitive hemopoiesis / histone H3K4 methyltransferase activity / Cardiogenesis / anterior/posterior pattern specification / T-helper 2 cell differentiation / exploration behavior / embryonic hemopoiesis / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / membrane depolarization / negative regulation of fibroblast proliferation / cellular response to transforming growth factor beta stimulus / spleen development / homeostasis of number of cells within a tissue / : / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / gluconeogenesis / skeletal system development / : / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / mitotic spindle / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / fibroblast proliferation / methylation / histone binding / regulation of cell cycle / apoptotic process / chromatin binding / 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 / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. ...KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / PHD-finger / Zinc finger PHD-type signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger PHD-type profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Histone-lysine N-methyltransferase 2A / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsSong, J.J. / Kingston, R.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: WDR5 Interacts with Mixed Lineage Leukemia (MLL) Protein via the Histone H3-binding Pocket.
Authors: Song, J.J. / Kingston, R.E.
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: Mixed-lineage leukemia protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6124
Polymers36,4202
Non-polymers1922
Water4,810267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-5.2 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.440, 98.290, 80.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-580-

HOH

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Components

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


Mass: 34916.590 Da / Num. of mol.: 1 / Fragment: UNP residues 25-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pGEX6p_1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61964
#2: Protein/peptide Mixed-lineage leukemia protein 1 / MLL1


Mass: 1503.705 Da / Num. of mol.: 1 / Fragment: UNP residues 2675-2687 / Source method: obtained synthetically
Details: Synthetic peptide following the sequence position 2675-2687 of UniProt entry Q59FF2 (Q59FF2_HUMAN)
References: UniProt: Q59FF2, UniProt: Q03164*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM HEPES, 15-20% PEG 3350, 60mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2008
RadiationMonochromator: 100 um / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. all: 64701 / Num. obs: 65115 / % possible obs: 99 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 36.1
Reflection shellResolution: 1.37→1.41 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / % possible all: 90.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H13

2h13


Resolution: 1.37→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.1998 3198
Rwork0.1903 -
obs0.1903 64701
all-64701
Refinement stepCycle: LAST / Resolution: 1.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 10 267 2676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004589
X-RAY DIFFRACTIONc_angle_deg1.89777
LS refinement shellResolution: 1.37→1.42 Å /
Num. reflection% reflection
obs5828 99 %

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