[English] 日本語
Yorodumi
- PDB-4l58: Crystal structure of the MLL5 PHD finger in complex with H3K4me3 -

+
Open data


ID or keywords:

Loading...

-
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 / : / neutrophil activation / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / histone H3K4me3 reader activity ...Set3 complex / Rpd3L-Expanded complex / negative regulation of chromosome condensation / Barr body / : / neutrophil activation / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / histone H3K4me3 reader activity / neutrophil mediated immunity / oocyte maturation / nucleosomal DNA binding / nucleus organization / : / spermatid development / positive regulation of G1/S transition of mitotic cell cycle / single fertilization / 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 / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / erythrocyte differentiation / 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 / euchromatin / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / multicellular organism growth / male gonad development / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / 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 / Amyloid fiber formation / protein heterodimerization activity / 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 / Herpes Virus-1 / SET domain / SET domain superfamily / SET domain profile. / SET domain / 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 / Herpes Virus-1 / SET domain / SET domain superfamily / SET domain profile. / SET domain / 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 domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more