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- PDB-7w6i: The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L... -

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Basic information

Entry
Database: PDB / ID: 7w6i
TitleThe crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide
Components
  • Histone H3.3C
  • Histone-lysine N-methyltransferase 2A
  • Retinoblastoma-binding protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
KeywordsPROTEIN BINDING / MLL family methyltransferases / product specificity / F/Y switch
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity / MLL1/2 complex / Set1C/COMPASS complex / definitive hemopoiesis / histone H3K4 methyltransferase activity / embryonic hemopoiesis / T-helper 2 cell differentiation / exploration behavior / anterior/posterior pattern specification / nucleosomal DNA binding / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / hemopoiesis / MLL1 complex / membrane depolarization / negative regulation of fibroblast proliferation / spleen development / cellular response to transforming growth factor beta stimulus / homeostasis of number of cells within a tissue / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / Deactivation of the beta-catenin transactivating complex / lysine-acetylated histone binding / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / visual learning / protein modification process / beta-catenin binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / response to estrogen / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / protein-containing complex assembly / fibroblast proliferation / methylation / histone binding / transcription cis-regulatory region binding / protein heterodimerization activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 ...: / : / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / ASH2, PHD zinc finger / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / 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 / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain / SET domain superfamily / SET domain profile. / SET domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Zinc finger, FYVE/PHD-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase 2A / Retinoblastoma-binding protein 5 / Histone H3.3C / Set1/Ash2 histone methyltransferase complex subunit ASH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsZhao, L. / Li, Y. / Chen, Y.
Funding support China, 5items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37010303 China
National Natural Science Foundation of China (NSFC)31670748 China
National Natural Science Foundation of China (NSFC)31970576 China
National Natural Science Foundation of China (NSFC)32071195 China
National Natural Science Foundation of China (NSFC)31900934 China
CitationJournal: Mol.Cell / Year: 2022
Title: Structural basis for product specificities of MLL family methyltransferases.
Authors: Li, Y. / Zhao, L. / Zhang, Y. / Wu, P. / Xu, Y. / Mencius, J. / Zheng, Y. / Wang, X. / Xu, W. / Huang, N. / Ye, X. / Lei, M. / Shi, P. / Tian, C. / Peng, C. / Li, G. / Liu, Z. / Quan, S. / Chen, Y.
History
DepositionDec 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Set1/Ash2 histone methyltransferase complex subunit ASH2
C: Histone-lysine N-methyltransferase 2A
F: Retinoblastoma-binding protein 5
B: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6936
Polymers43,2434
Non-polymers4502
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.777, 44.422, 120.097
Angle α, β, γ (deg.)90.000, 107.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein


Mass: 20597.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBL3
#2: Protein Histone-lysine N-methyltransferase 2A


Mass: 18314.207 Da / Num. of mol.: 1 / Mutation: N3861I,Q3867L,C3882SS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03164

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Protein/peptide , 2 types, 2 molecules FB

#3: Protein/peptide Retinoblastoma-binding protein 5 / RBBP-5 / Retinoblastoma-binding protein RBQ-3


Mass: 3255.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP5, RBQ3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15291
#4: Protein/peptide Histone H3.3C / H3K4me1 peptide


Mass: 1076.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2

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Non-polymers , 3 types, 47 molecules

#5: 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 12247 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.081 / Rrim(I) all: 0.175 / Χ2: 0.588 / Net I/σ(I): 3.2 / Num. measured all: 55070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.643.70.84911530.5860.4940.990.57398.1
2.64-2.754.30.7712410.6070.4080.8760.62798.9
2.75-2.874.60.58211990.7760.3020.6580.59899.4
2.87-3.024.70.39712110.8930.2040.4480.5499.3
3.02-3.214.50.25812110.8940.1380.2940.57399.7
3.21-3.464.40.20112200.9630.1070.2290.68399.8
3.46-3.814.90.13412330.9810.0680.1510.58299.7
3.81-4.364.70.09712570.9890.050.110.6399.8
4.36-5.494.40.0712470.9930.0380.080.492100
5.49-504.50.07412750.9920.0380.0830.57999.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F6L

5f6l


Resolution: 2.56→38.18 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1215 9.94 %
Rwork0.1977 11013 -
obs0.2024 12228 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.59 Å2 / Biso mean: 45.3563 Å2 / Biso min: 20.07 Å2
Refinement stepCycle: final / Resolution: 2.56→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 27 45 2982
Biso mean--63.79 36.92 -
Num. residues----362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.56-2.670.34421120.30831034114684
2.67-2.790.31611380.27361225136399
2.79-2.930.29071400.25821253139399
2.93-3.120.26831310.238812111342100
3.12-3.360.25281370.21591240137799
3.36-3.70.26871330.19791250138399
3.7-4.230.23521400.170212371377100
4.23-5.320.19321400.145312691409100
5.33-38.180.21871440.18361294143899

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