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

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Basic information

Entry
Database: PDB / ID: 3uvl
TitleCrystal structure of WDR5 in complex with the WDR5-interacting motif of MLL3
Components
  • Histone-lysine N-methyltransferase MLL3
  • 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 / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / 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 / acyltransferase activity / histone methyltransferase activity / 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 / response to electrical stimulus / 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 / methylation / transcription coactivator activity / 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 / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / FY-rich, N-terminal ...Histone-lysine N-methyltransferase 2C / KMT2C, ePHD1 / KMT2C, ePHD2 / : / : / : / DHHC domain profile. / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / 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 / 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 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / 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 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 MLL3


Theoretical massNumber of molelcules
Total (without water)35,9012
Polymers35,9012
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-5 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.980, 86.221, 40.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 MLL3 / Homologous to ALR protein / Lysine N-methyltransferase 2C / KMT2C / Myeloid/lymphoid or mixed- ...Homologous to ALR protein / Lysine N-methyltransferase 2C / KMT2C / Myeloid/lymphoid or mixed-lineage leukemia protein 3


Mass: 1106.254 Da / Num. of mol.: 1 / Fragment: WDR5-interacting motif (UNP residues 4707-4717) / Mutation: C4708S,S4711A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q8NEZ4, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 323 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M ammonium acetate, 25% PEG3350, 0.1 M Bis-Tris, pH 8.5, 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: 2.2→54 Å / Num. all: 15066 / Num. obs: 14659 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 41.96 Å2 / Rsym value: 0.075 / Net I/σ(I): 41
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.165 / % possible all: 81.6

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Processing

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

2h13


Resolution: 2.2→40.49 Å / Cor.coef. Fo:Fc: 0.9594 / Cor.coef. Fo:Fc free: 0.9275 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 735 5.03 %RANDOM
Rwork0.1696 ---
obs0.1722 14601 --
all-15066 --
Displacement parametersBiso mean: 39.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.1001 Å20 Å20 Å2
2---0.6935 Å20 Å2
3---1.7936 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 0 180 2577
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d830SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes349HARMONIC5
X-RAY DIFFRACTIONt_it2452HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion328SEMIHARMONIC5
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_contact2884SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2452HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3323HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion16.57
LS refinement shellResolution: 2.2→2.38 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2566 125 4.68 %
Rwork0.1878 2548 -
all0.1911 2673 -
Refinement TLS params.Method: refined / Origin x: -12.5935 Å / Origin y: 23.3525 Å / Origin z: -8.3531 Å
111213212223313233
T-0.0484 Å2-0.0109 Å20.0051 Å2--0.0509 Å20.0153 Å2---0.0254 Å2
L1.5193 °20.0394 °2-0.1849 °2-0.722 °2-0.2296 °2--0.3319 °2
S-0.0568 Å °-0.0102 Å °-0.1911 Å °-0.0693 Å °0.0604 Å °0.0024 Å °0.0374 Å °-0.0163 Å °-0.0036 Å °
Refinement TLS groupSelection details: { A|31 - A|334 }

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