[English] 日本語
Yorodumi
- PDB-2kyu: The solution structure of the PHD3 finger of MLL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kyu
TitleThe solution structure of the PHD3 finger of MLL
ComponentsHistone-lysine N-methyltransferase MLL
KeywordsTRANSFERASE / PHD / CHROMATIN REGULATION / TRANSCRIPTION
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-cysteine methyltransferase activity / response to potassium ion / histone H3K4 trimethyltransferase activity / unmethylated CpG binding / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / definitive hemopoiesis ...negative regulation of DNA methylation-dependent heterochromatin formation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-cysteine methyltransferase activity / response to potassium ion / histone H3K4 trimethyltransferase activity / unmethylated CpG binding / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / definitive hemopoiesis / histone H3K4 methyltransferase activity / regulation of short-term neuronal synaptic plasticity / anterior/posterior pattern specification / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / embryonic hemopoiesis / T-helper 2 cell differentiation / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / minor groove of adenine-thymine-rich DNA binding / exploration behavior / MLL1 complex / cellular response to transforming growth factor beta stimulus / membrane depolarization / negative regulation of fibroblast proliferation / spleen development / homeostasis of number of cells within a tissue / Transferases; Transferring one-carbon groups; Methyltransferases / transcription initiation-coupled chromatin remodeling / post-embryonic development / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / protein-containing complex assembly / fibroblast proliferation / methylation / apoptotic process / chromatin binding / 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 / cytosol
Similarity search - Function
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. ...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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Herpes Virus-1 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPark, S. / Bushweller, J.H.
CitationJournal: Biochemistry / Year: 2010
Title: The PHD3 domain of MLL acts as a CYP33-regulated switch between MLL-mediated activation and repression.
Authors: Park, S. / Osmers, U. / Raman, G. / Schwantes, R.H. / Diaz, M.O. / Bushweller, J.H.
History
DepositionJun 8, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_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 MLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8503
Polymers7,7201
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Histone-lysine N-methyltransferase MLL / Zinc finger protein HRX / ALL-1 / Trithorax-like protein / Lysine N-methyltransferase 2A / KMT2A / ...Zinc finger protein HRX / ALL-1 / Trithorax-like protein / Lysine N-methyltransferase 2A / KMT2A / CXXC-type zinc finger protein 7


Mass: 7719.636 Da / Num. of mol.: 1 / Fragment: PHD3 finger (UNP residues 1564-1628)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL, ALL1, CXXC7, HRX, HTRX, KMT2A, MLL1, TRX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03164
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY
1913D HNHA
11013D C(CO)NH
11113D TROSY-HNCO
11213D TROSY-HNCO

-
Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] PHD3, 100 uM ZINC ION, 25 mM potassium phosphate, 3 mM DTT, 50 mM sodium chloride, 1 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPHD3-1[U-98% 13C; U-98% 15N]1
100 uMZINC ION-21
25 mMpotassium phosphate-31
3 mMDTT-41
50 mMsodium chloride-51
1 mMsodium azide-61
Sample conditionspH: 6.9 / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Varian Avance / Manufacturer: Varian / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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