[English] 日本語
Yorodumi
- PDB-9atn: NMR structure of the MLL4 PHD2/3 fingers in complex with ASXL2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9atn
TitleNMR structure of the MLL4 PHD2/3 fingers in complex with ASXL2
Components
  • Histone-lysine N-methyltransferase 2D
  • Polycomb group protein ASXL2
KeywordsTRANSFERASE/PROTEIN BINDING / MLL4 / transcription / PROTEIN BINDING / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


beta-catenin-TCF complex assembly / PR-DUB complex / oocyte growth / positive regulation of peroxisome proliferator activated receptor signaling pathway / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / peroxisome proliferator activated receptor binding ...beta-catenin-TCF complex assembly / PR-DUB complex / oocyte growth / positive regulation of peroxisome proliferator activated receptor signaling pathway / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / peroxisome proliferator activated receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / oogenesis / Formation of WDR5-containing histone-modifying complexes / positive regulation of fat cell differentiation / heterochromatin formation / Deactivation of the beta-catenin transactivating complex / animal organ morphogenesis / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / UCH proteinases / histone binding / methylation / transcription coactivator activity / transcription cis-regulatory region binding / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx ...Histone-lysine N-methyltransferase 2D / KMT2D, ePHD1 domain / KMT2D, ePHD2 domain / : / : / Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / 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 / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / PHD-zinc-finger like domain / 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 / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone-lysine N-methyltransferase 2D / Putative Polycomb group protein ASXL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsZhang, Y. / Zandian, M. / Kutateladze, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: Nat Commun / Year: 2024
Title: ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers.
Authors: Zhang, Y. / Xie, G. / Lee, J.E. / Zandian, M. / Sudarshan, D. / Estavoyer, B. / Benz, C. / Viita, T. / Asgaritarghi, G. / Lachance, C. / Messmer, C. / Simonetti, L. / Sinha, V.K. / Lambert, ...Authors: Zhang, Y. / Xie, G. / Lee, J.E. / Zandian, M. / Sudarshan, D. / Estavoyer, B. / Benz, C. / Viita, T. / Asgaritarghi, G. / Lachance, C. / Messmer, C. / Simonetti, L. / Sinha, V.K. / Lambert, J.P. / Chen, Y.W. / Wang, S.P. / Ivarsson, Y. / Affar, E.B. / Cote, J. / Ge, K. / Kutateladze, T.G.
History
DepositionFeb 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase 2D
B: Polycomb group protein ASXL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2646
Polymers13,0022
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area6720 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Histone-lysine N-methyltransferase 2D / Lysine N-methyltransferase 2D / ALL1-related protein / Myeloid/lymphoid or mixed-lineage leukemia protein 2


Mass: 11014.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2D, ALR, MLL2, MLL4 / Production host: Escherichia coli (E. coli)
References: UniProt: O14686, [histone H3]-lysine4 N-methyltransferase
#2: Protein/peptide Polycomb group protein ASXL2 / Additional sex combs-like protein 2


Mass: 1987.347 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASXL2, ASXH2, KIAA1685 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76L83
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1141isotropic12D 1H-15N HSQC
1121isotropic12D 1H-13C HSQC aliphatic
1131isotropic12D 1H-13C HSQC aromatic
151isotropic13D HNCA
111isotropic13D HN(CA)CB
1151isotropic13D HN(CO)CA
121isotropic13D CBCA(CO)NH
131isotropic13D C(CO)NH
141isotropic13D HBHA(CO)NH
161isotropic13D H(CCO)NH
1101isotropic13D 1H-15N TOCSY
1111isotropic13D (H)CCH-TOCSY
171isotropic23D 1H-15N NOESY
181isotropic23D 1H-13C NOESY aromatic
191isotropic23D 1H-13C NOESY aliphatic

-
Sample preparation

DetailsType: solution
Contents: 1.5 mM 13C, 15N MLL4 PHD2,3, 25 mM TRIS, 150 mM sodium chloride, 3 mM DTT, 93% H2O/7% D2O
Label: U-13C, U-15N MLL4 PHD2,3 - C-ASXL2 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMMLL4 PHD2,313C, 15N1
25 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
3 mMDTTnatural abundance1
Sample conditionsIonic strength: 150 mM / Label: NMR Buffer / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA9002

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 15

+
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://pdbjlvh1.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