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- PDB-4erz: X-ray structure of WDR5-MLL4 Win motif peptide binary complex -

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Basic information

Entry
Database: PDB / ID: 4erz
TitleX-ray structure of WDR5-MLL4 Win motif peptide binary complex
Components
  • Histone-lysine N-methyltransferase MLL4
  • WD repeat-containing protein 5
KeywordsTranscription/Transferase / WD40 / Win motif / beta propeller / 3-10 helix / MLL4 / lysine methyltransferase / RbBP5 / MLL1 / Ash2L / core complex / Histone / Transcription-Transferase complex
Function / homology
Function and homology information


[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / 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 / 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 / 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 / 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 / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
KMT2B, ePHD domain / Methyltransferase, trithorax / : / 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 ...KMT2B, ePHD domain / Methyltransferase, trithorax / : / 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 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / 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 / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain-like superfamily / 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 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Data collection
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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 MLL4
E: Histone-lysine N-methyltransferase MLL4
F: Histone-lysine N-methyltransferase MLL4


Theoretical massNumber of molelcules
Total (without water)107,6216
Polymers107,6216
Non-polymers00
Water9,926551
1
A: WD repeat-containing protein 5
E: Histone-lysine N-methyltransferase MLL4


Theoretical massNumber of molelcules
Total (without water)35,8742
Polymers35,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area11920 Å2
MethodPISA
2
B: WD repeat-containing protein 5
F: Histone-lysine N-methyltransferase MLL4


Theoretical massNumber of molelcules
Total (without water)35,8742
Polymers35,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area11820 Å2
MethodPISA
3
C: WD repeat-containing protein 5
D: Histone-lysine N-methyltransferase MLL4


Theoretical massNumber of molelcules
Total (without water)35,8742
Polymers35,8742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.030, 80.290, 87.630
Angle α, β, γ (deg.)90.00, 90.04, 90.00
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 MLL4 / Lysine N-methyltransferase 2D / KMT2D / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / ...Lysine N-methyltransferase 2D / KMT2D / Myeloid/lymphoid or mixed-lineage leukemia protein 4 / Trithorax homolog 2 / WW domain-binding protein 7 / WBP-7


Mass: 1569.786 Da / Num. of mol.: 3 / Fragment: UNP residues 2025-2517 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UMN6, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 7.6
Details: PEG3350, Ammonium Sulfate, HEPES, pH 7.6, 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 / Date: Feb 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 44.87 / Number: 719771 / Rmerge(I) obs: 0.079 / Χ2: 2.6 / D res high: 1.75 Å / D res low: 30 Å / Num. obs: 97077 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.743096.710.0493.4316.5
3.774.7498.810.0483.4196.9
3.293.7799.910.0543.647.2
2.993.2910010.063.4217.4
2.782.9910010.0693.2727.4
2.612.7810010.0762.9867.5
2.482.6110010.0852.7747.5
2.372.4810010.0962.6197.5
2.282.3710010.1052.5247.6
2.22.2810010.1152.4977.6
2.142.210010.1222.3927.6
2.072.1410010.1332.3157.6
2.022.0710010.1552.247.6
1.972.0210010.1812.2487.6
1.931.9710010.2112.1077.5
1.891.9310010.2562.2417.5
1.851.8910010.3162.037.5
1.811.8510010.3972.0567.5
1.781.8110010.4771.9777.5
1.751.7810010.5462.0267.5
ReflectionResolution: 1.75→30 Å / Num. obs: 97077 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.75-1.787.50.5461100
1.78-1.817.50.4771100
1.81-1.857.50.3971100
1.85-1.897.50.3161100
1.89-1.937.50.2561100
1.93-1.977.50.2111100
1.97-2.027.60.1811100
2.02-2.077.60.1551100
2.07-2.147.60.1331100
2.14-2.27.60.1221100
2.2-2.287.60.1151100
2.28-2.377.60.1051100
2.37-2.487.50.0961100
2.48-2.617.50.0851100
2.61-2.787.50.0761100
2.78-2.997.40.0691100
2.99-3.297.40.061100
3.29-3.777.20.054199.9
3.77-4.746.90.048198.8
4.74-306.50.049196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→27.24 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 4826 4.99 %
Rwork0.186 --
obs0.187 96631 99.5 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.45 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.1791 Å20 Å2-0.1456 Å2
2--3.032 Å20 Å2
3----5.2111 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 0 551 7886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077509
X-RAY DIFFRACTIONf_angle_d1.17410188
X-RAY DIFFRACTIONf_dihedral_angle_d12.8912652
X-RAY DIFFRACTIONf_chiral_restr0.0821146
X-RAY DIFFRACTIONf_plane_restr0.0061269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.26061650.2343001X-RAY DIFFRACTION99
1.7699-1.79070.31181800.23973017X-RAY DIFFRACTION100
1.7907-1.81250.24821740.2353004X-RAY DIFFRACTION99
1.8125-1.83550.27981360.22033088X-RAY DIFFRACTION99
1.8355-1.85960.29951560.22093060X-RAY DIFFRACTION99
1.8596-1.88510.24911460.21163060X-RAY DIFFRACTION100
1.8851-1.9120.2381540.20683128X-RAY DIFFRACTION100
1.912-1.94050.25961530.20282923X-RAY DIFFRACTION100
1.9405-1.97090.23051760.19123044X-RAY DIFFRACTION100
1.9709-2.00320.24061840.18873085X-RAY DIFFRACTION100
2.0032-2.03770.23151360.19413069X-RAY DIFFRACTION100
2.0377-2.07470.26131650.19683063X-RAY DIFFRACTION100
2.0747-2.11460.24461420.19873120X-RAY DIFFRACTION100
2.1146-2.15780.22141400.19123055X-RAY DIFFRACTION100
2.1578-2.20470.25171650.18593052X-RAY DIFFRACTION100
2.2047-2.25590.23161700.18043077X-RAY DIFFRACTION100
2.2559-2.31230.21881790.1913032X-RAY DIFFRACTION100
2.3123-2.37480.23981620.1913097X-RAY DIFFRACTION100
2.3748-2.44460.20041580.19373057X-RAY DIFFRACTION100
2.4446-2.52350.25021720.20563077X-RAY DIFFRACTION100
2.5235-2.61360.2241390.19893057X-RAY DIFFRACTION100
2.6136-2.71820.24191620.20113034X-RAY DIFFRACTION100
2.7182-2.84180.23931810.20883101X-RAY DIFFRACTION100
2.8418-2.99140.2221650.20293078X-RAY DIFFRACTION100
2.9914-3.17860.21931520.19463056X-RAY DIFFRACTION100
3.1786-3.42350.19211440.17373112X-RAY DIFFRACTION100
3.4235-3.76730.18761710.16423087X-RAY DIFFRACTION100
3.7673-4.31050.16631620.15373056X-RAY DIFFRACTION99
4.3105-5.42380.161820.14493044X-RAY DIFFRACTION98
5.4238-27.2390.22081550.18823071X-RAY DIFFRACTION96

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