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- PDB-3p4f: Structural and biochemical insights into MLL1 core complex assemb... -

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Basic information

Entry
Database: PDB / ID: 3p4f
TitleStructural and biochemical insights into MLL1 core complex assembly and regulation.
Components
  • Histone-lysine N-methyltransferase MLL
  • Retinoblastoma-binding protein 5
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION / beta-propeller / scaffold / MLL1 / RbBP5
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 / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / 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 / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / definitive hemopoiesis / NSL complex / histone H3K4 methyltransferase activity / T-helper 2 cell differentiation / : / Cardiogenesis / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / regulation of tubulin deacetylation / : / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / regulation of embryonic development / 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 / Deactivation of the beta-catenin transactivating complex / gluconeogenesis / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / protein modification process / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / 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 / response to estrogen / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / histone binding / fibroblast proliferation / protein-containing complex assembly / transcription cis-regulatory region binding / regulation of cell cycle / apoptotic process / DNA damage response / chromatin binding / nucleolus / 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
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 ...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 / SET domain superfamily / SET domain / SET domain profile. / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / 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. / 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
WD repeat-containing protein 5 / Histone-lysine N-methyltransferase 2A / Retinoblastoma-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAvdic, V. / Zhang, P. / Lanouette, S. / Groulx, A. / Tremblay, V. / Brunzelle, J.B. / Couture, J.-F.
CitationJournal: Structure / Year: 2011
Title: Structural and biochemical insights into MLL1 core complex assembly.
Authors: Avdic, V. / Zhang, P. / Lanouette, S. / Groulx, A. / Tremblay, V. / Brunzelle, J. / Couture, J.-F.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Retinoblastoma-binding protein 5
C: Histone-lysine N-methyltransferase MLL


Theoretical massNumber of molelcules
Total (without water)37,0553
Polymers37,0553
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-10 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.850, 81.350, 81.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34707.367 Da / Num. of mol.: 1 / Fragment: unp residues 1-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Protein/peptide Retinoblastoma-binding protein 5 / RBBP-5 / Retinoblastoma-binding protein RBQ-3


Mass: 1284.280 Da / Num. of mol.: 1 / Fragment: unp residues 371-381 / Mutation: Y381D / Source method: obtained synthetically / Details: synthetic peptide (New England peptide) / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15291
#3: Protein/peptide Histone-lysine N-methyltransferase MLL / Zinc finger protein HRX / ALL-1 / Trithorax-like protein / Lysine N-methyltransferase 2A


Mass: 1063.190 Da / Num. of mol.: 1 / Fragment: unp residues 3761-3770 / Mutation: S3763A / Source method: obtained synthetically / Details: synthetic peptide (New England peptide) / Source: (synth.) Homo sapiens (human)
References: UniProt: Q03164, histone-lysine N-methyltransferase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 18, 2010
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→32.6 Å / Num. all: 15532 / Num. obs: 15413 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 5 / Biso Wilson estimate: 53.04 Å2 / Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
BUSTER2.8.0refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H14

2h14


Resolution: 2.35→32.57 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.9255 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 771 5.01 %RANDOM
Rwork0.1938 ---
obs0.1965 15380 --
all-15413 --
Displacement parametersBiso mean: 42.58 Å2
Baniso -1Baniso -2Baniso -3
1--3.4452 Å20 Å20 Å2
2--2.0575 Å20 Å2
3---1.3877 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.35→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 0 244 2718
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0125322
X-RAY DIFFRACTIONt_angle_deg1.334392
X-RAY DIFFRACTIONt_trig_c_planes592
X-RAY DIFFRACTIONt_gen_planes3625
X-RAY DIFFRACTIONt_it253220
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion17.28
X-RAY DIFFRACTIONt_chiral_improper_torsion3405
X-RAY DIFFRACTIONt_ideal_dist_contact29754
LS refinement shellResolution: 2.35→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3354 148 5.46 %
Rwork0.2572 2562 -
all0.2618 2710 -

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