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- PDB-4esg: X-ray structure of WDR5-MLL1 Win motif peptide binary complex -

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Basic information

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


protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity / Set1C/COMPASS complex ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity / Set1C/COMPASS complex / MLL1/2 complex / T-helper 2 cell differentiation / definitive hemopoiesis / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / positive regulation of gluconeogenesis / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / methylated histone binding / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / skeletal system development / gluconeogenesis / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / HATs acetylate histones / histone binding / fibroblast proliferation / methylation / protein-containing complex assembly / regulation of cell cycle / apoptotic process / chromatin binding / 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 / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. ...KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / 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 profile. / bromo domain / Bromodomain / 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 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 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 1.3Feb 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: Histone-lysine N-methyltransferase MLL
D: Histone-lysine N-methyltransferase MLL


Theoretical massNumber of molelcules
Total (without water)72,3764
Polymers72,3764
Non-polymers00
Water11,295627
1
A: WD repeat-containing protein 5
D: Histone-lysine N-methyltransferase MLL


Theoretical massNumber of molelcules
Total (without water)36,1882
Polymers36,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area12420 Å2
MethodPISA
2
B: WD repeat-containing protein 5
C: Histone-lysine N-methyltransferase MLL


Theoretical massNumber of molelcules
Total (without water)36,1882
Polymers36,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.606, 80.154, 83.517
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 31:334 )
211chain 'B' and (resseq 31:334 )
112chain 'C' and (resseq 3755:3770 )
212chain 'D' and (resseq 3755:3770 )

NCS ensembles :
ID
1
2

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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.: 2 / 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 MLL / ALL-1 / CXXC-type zinc finger protein 7 / Lysine N-methyltransferase 2A / KMT2A / Trithorax-like ...ALL-1 / CXXC-type zinc finger protein 7 / Lysine N-methyltransferase 2A / KMT2A / Trithorax-like protein / Zinc finger protein HRX / MLL cleavage product N320 / N-terminal cleavage product of 320 kDa / p320 / MLL cleavage product C180 / C-terminal cleavage product of 180 kDa / p180


Mass: 1884.103 Da / Num. of mol.: 2 / Fragment: UNP residues 3755-3771 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q03164, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 294 K / Method: hanging drop / pH: 7.2
Details: PEG3350, Ammonium Sulfate, HEPES, pH 7.2, 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: 6.7 % / Av σ(I) over netI: 28.53 / Number: 371865 / Rmerge(I) obs: 0.111 / Χ2: 2.37 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 55756 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665099.910.0594.2336.7
2.913.6610010.0693.2697.3
2.542.9110010.12.6937.5
2.312.5410010.142.2777.5
2.142.3110010.1722.0267.6
2.022.1410010.2221.9417.5
1.912.0210010.2881.8017.3
1.831.9110010.3831.7056.5
1.761.8399.810.4741.5285.2
1.71.7693.810.4951.2963.4
ReflectionResolution: 1.7→50 Å / Num. obs: 55756 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.763.40.495193.8
1.76-1.835.20.474199.8
1.83-1.916.50.3831100
1.91-2.027.30.2881100
2.02-2.147.50.2221100
2.14-2.317.60.1721100
2.31-2.547.50.141100
2.54-2.917.50.11100
2.91-3.667.30.0691100
3.66-506.70.059199.9

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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: 1.7→40.08 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 2822 5.08 %
Rwork0.162 --
obs0.164 55600 99.4 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.33 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso mean: 17.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.7255 Å2-0 Å2-0.5078 Å2
2---3.134 Å2-0 Å2
3---3.8595 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4942 0 0 627 5569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095070
X-RAY DIFFRACTIONf_angle_d1.2226882
X-RAY DIFFRACTIONf_dihedral_angle_d12.1161798
X-RAY DIFFRACTIONf_chiral_restr0.086774
X-RAY DIFFRACTIONf_plane_restr0.005860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2357X-RAY DIFFRACTIONPOSITIONAL
12B2357X-RAY DIFFRACTIONPOSITIONAL0.068
21C118X-RAY DIFFRACTIONPOSITIONAL
22D118X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.33111330.28372410X-RAY DIFFRACTION93
1.7293-1.76080.32611490.25372635X-RAY DIFFRACTION97
1.7608-1.79460.24321330.23782573X-RAY DIFFRACTION99
1.7946-1.83130.24391460.1992682X-RAY DIFFRACTION100
1.8313-1.87110.23871360.18192626X-RAY DIFFRACTION100
1.8711-1.91460.19081180.1672661X-RAY DIFFRACTION100
1.9146-1.96250.19931470.1562615X-RAY DIFFRACTION100
1.9625-2.01560.19991520.16412635X-RAY DIFFRACTION100
2.0156-2.07490.18491460.16422651X-RAY DIFFRACTION100
2.0749-2.14180.20681270.16392720X-RAY DIFFRACTION100
2.1418-2.21840.17831480.15522572X-RAY DIFFRACTION100
2.2184-2.30720.23051570.15372639X-RAY DIFFRACTION100
2.3072-2.41220.21151570.16712661X-RAY DIFFRACTION100
2.4122-2.53930.19051600.16212632X-RAY DIFFRACTION100
2.5393-2.69840.20831380.16042637X-RAY DIFFRACTION100
2.6984-2.90670.19841450.16452662X-RAY DIFFRACTION100
2.9067-3.19910.17111200.15452691X-RAY DIFFRACTION100
3.1991-3.66170.13991370.13162666X-RAY DIFFRACTION100
3.6617-4.61230.15341310.13292688X-RAY DIFFRACTION100
4.6123-40.08810.18841420.17142722X-RAY DIFFRACTION100

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