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

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Basic information

Entry
Database: PDB / ID: 3uvk
TitleCrystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2
Components
  • Histone-lysine N-methyltransferase MLL2
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION / trithorax / chromatin biology / beta-propeller / scaffolding / histone H3 / nucleus
Function / homology
Function and homology information


beta-catenin-TCF complex assembly / oocyte growth / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex ...beta-catenin-TCF complex assembly / oocyte growth / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / oogenesis / positive regulation of intracellular estrogen receptor signaling pathway / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / response to estrogen / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / heterochromatin formation / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / methylation / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of cell population proliferation / 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 / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / 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 ...Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / 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 / WDR5 beta-propeller domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / PHD-zinc-finger like domain / 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 / Ring finger / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / WD domain, G-beta repeat / 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. / 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 2D / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 ...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: Histone-lysine N-methyltransferase MLL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2764
Polymers35,9712
Non-polymers3052
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-18 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.827, 68.496, 87.815
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 / 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 MLL2 / ALL1-related protein / Lysine N-methyltransferase 2B / KMT2B / Myeloid/lymphoid or mixed-lineage ...ALL1-related protein / Lysine N-methyltransferase 2B / KMT2B / Myeloid/lymphoid or mixed-lineage leukemia protein 2


Mass: 1176.387 Da / Num. of mol.: 1 / Fragment: WDR5-interacting motif (UNP residues 5337-5347) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O14686, histone-lysine N-methyltransferase
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 323 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium sulfate, 24% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K

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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: 1.4→31.907 Å / Num. all: 55849 / Num. obs: 57766 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.041 / Net I/σ(I): 47.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.355 / % possible all: 81.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H13

2h13


Resolution: 1.4→31.907 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.919 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19242 2917 5.1 %RANDOM
Rwork0.15136 ---
obs0.15339 54732 --
all-55849 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0 Å2
2--0.11 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→31.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 19 206 2617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222509
X-RAY DIFFRACTIONr_angle_refined_deg2.2061.9523408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7415320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13625.10992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03815437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.715154
X-RAY DIFFRACTIONr_chiral_restr0.1610.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211817
X-RAY DIFFRACTIONr_mcbond_it2.691.51570
X-RAY DIFFRACTIONr_mcangle_it3.70922541
X-RAY DIFFRACTIONr_scbond_it5.2493939
X-RAY DIFFRACTIONr_scangle_it7.2964.5862
X-RAY DIFFRACTIONr_rigid_bond_restr2.84832509
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 183 -
Rwork0.274 3397 -
obs--83.74 %
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)
10.4089-0.0746-0.09470.12190.13840.99010.0226-0.0244-0.001-0.03820.0064-0.0131-0.00940.0028-0.0290.01930.0048-0.00630.0126-0.01120.018-12.4279.671-17.574
26.3168-1.65384.64341.233-1.37183.4643-0.3118-0.14960.43130.16320.04930.0442-0.2877-0.12570.26250.12980.0440.04280.01740.00570.0888-17.66924.659-20.73
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 334
2X-RAY DIFFRACTION2B5062 - 5072

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