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- PDB-4z4p: Structure of the MLL4 SET Domain -

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Basic information

Entry
Database: PDB / ID: 4z4p
TitleStructure of the MLL4 SET Domain
ComponentsHistone-lysine N-methyltransferase 2D
KeywordsTRANSFERASE / SET Domain Methyltransferase
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 / MLL3/4 complex / histone H3K4 methyltransferase activity / positive regulation of intracellular estrogen receptor signaling pathway / oogenesis / Formation of WDR5-containing histone-modifying complexes ...beta-catenin-TCF complex assembly / oocyte growth / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / positive regulation of intracellular estrogen receptor signaling pathway / oogenesis / Formation of WDR5-containing histone-modifying complexes / 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 / heterochromatin formation / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / methylation / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
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 / Beta-clip-like / SET 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 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain superfamily / SET domain profile. / SET domain / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Beta Complex / 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 / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase 2D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Z. / Mittal, A. / Reid, J. / Reich, S. / Gamblin, S.J. / Wilson, J.R.
CitationJournal: Structure / Year: 2015
Title: Evolving Catalytic Properties of the MLL Family SET Domain.
Authors: Zhang, Y. / Mittal, A. / Reid, J. / Reich, S. / Gamblin, S.J. / Wilson, J.R.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase 2D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1543
Polymers19,7041
Non-polymers4502
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.299, 40.692, 50.965
Angle α, β, γ (deg.)90.00, 109.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase 2D / Lysine N-methyltransferase 2D / ALL1-related protein / Myeloid/lymphoid or mixed-lineage leukemia protein 2


Mass: 19704.355 Da / Num. of mol.: 1 / Fragment: UNP residues 5385-5539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2D, ALR, MLL2, MLL4 / Production host: Escherichia coli #1/H766 (bacteria)
References: UniProt: O14686, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl 20 % Ethanol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2011
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→47.96 Å / Num. obs: 7566 / % possible obs: 98.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 8.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o9s

1o9s


Resolution: 2.2→47.96 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 0.017 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24247 366 4.9 %RANDOM
Rwork0.19348 ---
obs0.19567 7143 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.523 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0 Å20.16 Å2
2---0.43 Å2-0 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 27 60 1422
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 34 -
Rwork0.203 502 -
obs--94.53 %

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