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- PDB-5m25: Modulation of MLL1 Methyltransferase Activity -

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Basic information

Entry
Database: PDB / ID: 5m25
TitleModulation of MLL1 Methyltransferase Activity
ComponentsWD repeat-containing protein 5
KeywordsTRANSFERASE / MLL1 Methyltransferase peptide complex WDR5
Function / homology
Function and homology information


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 ...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 / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / 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 / 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 / nucleoplasm / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-7DU / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSrinivasan, V.
CitationJournal: Chem Sci / Year: 2017
Title: Controlled inhibition of methyltransferases using photoswitchable peptidomimetics: towards an epigenetic regulation of leukemia.
Authors: Albert, L. / Xu, J. / Wan, R. / Srinivasan, V. / Dou, Y. / Vazquez, O.
History
DepositionOct 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 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: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7392
Polymers48,1121
Non-polymers6271
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.714, 85.917, 39.276
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 / BMP2-induced 3-kb gene protein


Mass: 48112.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P61964
#2: Chemical ChemComp-7DU / (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]propanoyl]amino]-5-carbamimidamido-~{N}-[(2~{S})-1-[[4-[(~{E})-[4-(hydroxymethyl)phenyl]diazenyl]phenyl]methylamino]-1-oxidanylidene-propan-2-yl]pentanamide


Mass: 626.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H42N10O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.02 M carboxylic acid 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.43→42.96 Å / Num. obs: 19553 / % possible obs: 98.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.43→2.56 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eg6

3eg6


Resolution: 2.43→42.959 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.57 / Phase error: 25.03
RfactorNum. reflection% reflection
Rfree0.2482 980 5.01 %
Rwork0.1761 --
obs0.1795 19553 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.43→42.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 45 98 2469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082428
X-RAY DIFFRACTIONf_angle_d1.1963291
X-RAY DIFFRACTIONf_dihedral_angle_d15.446875
X-RAY DIFFRACTIONf_chiral_restr0.044365
X-RAY DIFFRACTIONf_plane_restr0.004406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4301-2.55820.45951400.33272585X-RAY DIFFRACTION96
2.5582-2.71840.30861400.21752675X-RAY DIFFRACTION100
2.7184-2.92830.24371400.17782694X-RAY DIFFRACTION100
2.9283-3.22290.24681420.1582688X-RAY DIFFRACTION99
3.2229-3.6890.20281360.14112598X-RAY DIFFRACTION97
3.689-4.64690.20681360.14472689X-RAY DIFFRACTION99
4.6469-42.96520.21861460.16492644X-RAY DIFFRACTION98

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