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- PDB-4l58: Crystal structure of the MLL5 PHD finger in complex with H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 4l58
TitleCrystal structure of the MLL5 PHD finger in complex with H3K4me3
Components
  • Histone H3 peptide
  • Histone-lysine N-methyltransferase MLL5
KeywordsTRANSFERASE
Function / homology
Function and homology information


Set3 complex / Rpd3L-Expanded complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / neutrophil activation / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / neutrophil mediated immunity ...Set3 complex / Rpd3L-Expanded complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / neutrophil activation / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / neutrophil mediated immunity / oocyte maturation / nucleosomal DNA binding / nucleus organization / spermatid development / single fertilization / positive regulation of G1/S transition of mitotic cell cycle / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / : / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / erythrocyte differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / multicellular organism growth / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription coactivator activity / chromosome, telomeric region / cell population proliferation / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / centrosome / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / protein-containing complex / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
KMT2E, SET domain / PhD finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Herpes Virus-1 / Zinc finger, PHD-type, conserved site ...KMT2E, SET domain / PhD finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.3 / Inactive histone-lysine N-methyltransferase 2E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsTong, Q. / Ali, M. / Kutateladze, T.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular basis for chromatin binding and regulation of MLL5.
Authors: Ali, M. / Rincon-Arano, H. / Zhao, W. / Rothbart, S.B. / Tong, Q. / Parkhurst, S.M. / Strahl, B.D. / Deng, L.W. / Groudine, M. / Kutateladze, T.G.
History
DepositionJun 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase MLL5
B: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6684
Polymers9,5372
Non-polymers1312
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-6 kcal/mol
Surface area4780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.286, 43.638, 52.856
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 Histone-lysine N-methyltransferase MLL5 / Lysine N-methyltransferase 2E / KMT2E / Myeloid/lymphoid or mixed-lineage leukemia protein 5


Mass: 8186.495 Da / Num. of mol.: 1 / Fragment: PHD-type zinc finger domain residues 117-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL5, KMT2E / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IZD2, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3 peptide / H3K4me3 peptide


Mass: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The modified peptide was synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.14 mM potassium acetate and 35 % PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 18, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→33 Å / Num. obs: 22776 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.64 Å2
Reflection shellResolution: 1.48→1.55 Å / % possible all: 67.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→33 Å / SU ML: 0.08 / σ(F): 1.36 / Phase error: 12.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1402 1138 5 %RANDOM
Rwork0.1251 ---
obs0.1258 22776 97.59 %-
all-22776 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms591 0 2 125 718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004599
X-RAY DIFFRACTIONf_angle_d1.054804
X-RAY DIFFRACTIONf_dihedral_angle_d15.979235
X-RAY DIFFRACTIONf_chiral_restr0.06786
X-RAY DIFFRACTIONf_plane_restr0.003104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4797-1.5470.16241260.15052400X-RAY DIFFRACTION86
1.547-1.62860.15451470.11732734X-RAY DIFFRACTION98
1.6286-1.73060.14111450.10092716X-RAY DIFFRACTION99
1.7306-1.86420.13061390.10092730X-RAY DIFFRACTION99
1.8642-2.05180.13421430.12062772X-RAY DIFFRACTION99
2.0518-2.34870.13361430.1232750X-RAY DIFFRACTION100
2.3487-2.95880.14211470.13112759X-RAY DIFFRACTION100
2.9588-33.65990.14011480.13472777X-RAY DIFFRACTION100

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