[English] 日本語
Yorodumi
- PDB-2l43: Structural basis for histone code recognition by BRPF2-PHD1 finger -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l43
TitleStructural basis for histone code recognition by BRPF2-PHD1 finger
ComponentsHistone H3.3,LINKER,Bromodomain-containing protein 1
KeywordsTRANSCRIPTION / PHD finger / histone code
Function / homology
Function and homology information


histone H3-K14 acetyltransferase complex / nucleosomal DNA binding / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / response to electrical stimulus ...histone H3-K14 acetyltransferase complex / nucleosomal DNA binding / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / Inhibition of DNA recombination at telomere / telomere organization / histone reader activity / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / positive regulation of erythrocyte differentiation / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / perikaryon / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / dendrite / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
BRPF2, ePHD domain / BRPF2, PHD domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif ...BRPF2, ePHD domain / BRPF2, PHD domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bromodomain-containing protein 1 / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsQin, S. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: To be Published
Title: Recognition of unmodified histone H3 by the first PHD finger of Bromodomain-PHD finger protein 2 provides insights into the regulation of histone acetyltransferases MOZ and MORF
Authors: Qin, S. / Zhang, J. / Wu, J. / Shi, Y.
History
DepositionOct 1, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_software / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_nmr_software.name ..._entity.pdbx_description / _pdbx_nmr_software.name / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3.3,LINKER,Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9223
Polymers9,7911
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Histone H3.3,LINKER,Bromodomain-containing protein 1 / BR140-like protein / Bromodomain and PHD finger-containing protein 2


Mass: 9790.953 Da / Num. of mol.: 1 / Mutation: C29S, C36S
Source method: isolated from a genetically manipulated source
Details: chimeric protein of histone H3.3, linker, BRPF2 PHD1 domain
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B, BRD1, BRL, BRPF2
Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84243, UniProt: O95696
#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
Details: Solution structure of histone H3(1-12)-BRPF2 PHD1 chimeric protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D C(CO)NH
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D 1H-15N NOESY
1823D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM [U-100% 13C; U-100% 15N] protein-1, 1.6mM ZINC ION-2, 20mM Bis-Tris-3, 150mM sodium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
20.8mM [U-100% 13C; U-100% 15N] protein-5, 1.6mM ZINC ION-6, 20mM Bis-Tris-7, 150mM sodium chloride-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMprotein-1[U-100% 13C; U-100% 15N]1
1.6 mMZINC ION-21
20 mMBis-Tris-31
150 mMsodium chloride-41
0.8 mMprotein-5[U-100% 13C; U-100% 15N]2
1.6 mMZINC ION-62
20 mMBis-Tris-72
150 mMsodium chloride-82
Sample conditionsIonic strength: 0.15 / pH: 6.7 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddarddata analysis
Sparky3Goddardchemical shift assignment
Sparky3Goddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxchemical shift calculation
ProcheckNMRLaskowski and MacArthurdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1201 / NOE intraresidue total count: 464 / NOE long range total count: 301 / NOE medium range total count: 139 / NOE sequential total count: 297 / Hydrogen bond constraints total count: 28 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 31 / Protein psi angle constraints total count: 31
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

+
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