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- PDB-4erq: X-ray structure of WDR5-MLL2 Win motif peptide binary complex -

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Basic information

Entry
Database: PDB / ID: 4erq
TitleX-ray structure of WDR5-MLL2 Win motif peptide binary complex
Components
  • Histone-lysine N-methyltransferase MLL2
  • WD repeat-containing protein 5
KeywordsTranscription/Transferase / WD40 / Win motif peptide / beta propeller / 3-10 helix / lysine methyltransferase / RbBP5 / MLL1 / Ash2L / core complex / Histone / Transcription-Transferase complex
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 / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex ...beta-catenin-TCF complex assembly / oocyte growth / [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 / positive regulation of intracellular estrogen receptor signaling pathway / histone methyltransferase complex / regulation of tubulin deacetylation / oogenesis / 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 / heterochromatin formation / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / Deactivation of the beta-catenin transactivating complex / gluconeogenesis / Formation of the beta-catenin:TCF transactivating complex / 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 / response to estrogen / Neddylation / HATs acetylate histones / 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 / nucleoplasm / metal ion binding / 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 / 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
Histone-lysine N-methyltransferase 2D / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.906 Å
AuthorsDharmarajan, V. / Lee, J.-H. / Patel, A. / Skalnik, D.G. / Cosgrove, M.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for WDR5 interaction (Win) motif recognition in human SET1 family histone methyltransferases.
Authors: Dharmarajan, V. / Lee, J.H. / Patel, A. / Skalnik, D.G. / Cosgrove, M.S.
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
C: WD repeat-containing protein 5
D: Histone-lysine N-methyltransferase MLL2
E: Histone-lysine N-methyltransferase MLL2
F: Histone-lysine N-methyltransferase MLL2


Theoretical massNumber of molelcules
Total (without water)107,4146
Polymers107,4146
Non-polymers00
Water12,520695
1
A: WD repeat-containing protein 5
D: Histone-lysine N-methyltransferase MLL2


Theoretical massNumber of molelcules
Total (without water)35,8052
Polymers35,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area12180 Å2
MethodPISA
2
B: WD repeat-containing protein 5
E: Histone-lysine N-methyltransferase MLL2


Theoretical massNumber of molelcules
Total (without water)35,8052
Polymers35,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area12150 Å2
MethodPISA
3
C: WD repeat-containing protein 5
F: Histone-lysine N-methyltransferase MLL2


Theoretical massNumber of molelcules
Total (without water)35,8052
Polymers35,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.780, 80.790, 88.120
Angle α, β, γ (deg.)90.000, 90.1970, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34303.914 Da / Num. of mol.: 3 / Fragment: UNP residues 23-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIG3, WDR5 / Plasmid: pHIS paralell / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / 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: 1500.762 Da / Num. of mol.: 3 / Fragment: UNP residues 5333-5346 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O14686, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 7.3
Details: PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionRedundancy: 1 % / Av σ(I) over netI: 13.31 / Number: 773 / D res high: 1.9 Å / D res low: 30 Å / Num. obs: 772 / % possible obs: 1
Diffraction reflection shellHighest resolution: 1.9 Å / Lowest resolution: 30 Å / % possible obs: 1 % / Redundancy: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 76235 / % possible obs: 1 % / Redundancy: 1 % / Net I/σ(I): 9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.906→29.775 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8681 / SU ML: 0.19 / σ(F): 1.33 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 3835 5.03 %
Rwork0.1653 --
obs0.1671 76235 99.54 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.769 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 66.71 Å2 / Biso mean: 26.0178 Å2 / Biso min: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.2682 Å20 Å2-0.7638 Å2
2--0.2188 Å2-0 Å2
3---0.0493 Å2
Refinement stepCycle: LAST / Resolution: 1.906→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7356 0 0 695 8051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087527
X-RAY DIFFRACTIONf_angle_d1.13710209
X-RAY DIFFRACTIONf_chiral_restr0.0821155
X-RAY DIFFRACTIONf_plane_restr0.0051269
X-RAY DIFFRACTIONf_dihedral_angle_d11.7982679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.906-1.93040.2591110.20092426253789
1.9304-1.95580.27031340.202727212855100
1.9558-1.98260.25931490.196625912740100
1.9826-2.01090.26571440.185427322876100
2.0109-2.04090.26121390.180426642803100
2.0409-2.07280.23691180.183226912809100
2.0728-2.10680.21871420.174126652807100
2.1068-2.14310.25111430.180526992842100
2.1431-2.1820.20451490.169527192868100
2.182-2.2240.22861490.16626462795100
2.224-2.26940.23521550.173726562811100
2.2694-2.31870.21181380.184426792817100
2.3187-2.37260.26551270.186927132840100
2.3726-2.43190.24471460.181626962842100
2.4319-2.49760.22151500.178326772827100
2.4976-2.57110.19481430.179626362779100
2.5711-2.6540.22621620.186127012863100
2.654-2.74880.2321290.189227152844100
2.7488-2.85880.22281320.190826972829100
2.8588-2.98880.23151300.187427092839100
2.9888-3.14620.22041520.178626722824100
3.1462-3.34310.19561450.16927212866100
3.3431-3.60080.17681310.154126942825100
3.6008-3.96240.17251510.146626862837100
3.9624-4.53410.14451620.121127122874100
4.5341-5.70590.14981410.126727222863100
5.7059-29.7750.17141630.169627602923100

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