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- PDB-3uvm: Crystal structure of WDR5 in complex with the WDR5-interacting mo... -

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Basic information

Entry
Database: PDB / ID: 3uvm
TitleCrystal structure of WDR5 in complex with the WDR5-interacting motif of MLL4
Components
  • Histone-lysine N-methyltransferase MLL4
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION / trithorax / chromatin biology / beta-propeller / scaffolding / histone H3 / nucleus
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / MLL1/2 complex / Set1C/COMPASS complex / ATAC complex / NSL complex ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / MLL1/2 complex / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / mitotic spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / methylation / 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 / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
KMT2B, ePHD domain / 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 ...KMT2B, ePHD domain / 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. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / 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-like superfamily / Zinc finger, RING/FYVE/PHD-type / 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 / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Histone-lysine N-methyltransferase 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsZhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.-F.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases.
Authors: Zhang, P. / Lee, H. / Brunzelle, J.S. / Couture, J.F.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2May 30, 2012Group: Database references
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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: Histone-lysine N-methyltransferase MLL4


Theoretical massNumber of molelcules
Total (without water)35,9022
Polymers35,9022
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-5 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.527, 98.774, 79.740
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 / WDR5 / BMP2-induced 3-kb gene protein


Mass: 34794.449 Da / Num. of mol.: 1 / Fragment: UNP residues 21-334
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 Histone-lysine N-methyltransferase MLL4 / Lysine N-methyltransferase 2D / KMT2D / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / ...Lysine N-methyltransferase 2D / KMT2D / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax homolog 2 / WW domain-binding protein 7 / WBP-7


Mass: 1107.264 Da / Num. of mol.: 1 / Fragment: WDR5-interacting motif (UNP residues 2508-2517) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UMN6, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M ammonium sulfate, 25% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12718 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12718 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. all: 43154 / Num. obs: 42549 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 17.43 Å2 / Rsym value: 0.081 / Net I/σ(I): 21.1
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 6 / Rsym value: 0.422 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2H13

2h13


Resolution: 1.57→41.99 Å / Cor.coef. Fo:Fc: 0.9497 / Cor.coef. Fo:Fc free: 0.9456 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 2146 5.05 %RANDOM
Rwork0.1698 ---
obs0.1712 42525 --
all-43154 --
Displacement parametersBiso mean: 19.49 Å2
Baniso -1Baniso -2Baniso -3
1--3.1415 Å20 Å20 Å2
2---2.7565 Å20 Å2
3---5.898 Å2
Refine analyzeLuzzati coordinate error obs: 0.156 Å
Refinement stepCycle: LAST / Resolution: 1.57→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 0 170 2597
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d881SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2557HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion344SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3105SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2557HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3487HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion4.87
X-RAY DIFFRACTIONt_other_torsion15.83
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2392 138 5.16 %
Rwork0.1884 2539 -
all-2677 -

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