[English] 日本語
Yorodumi
- PDB-5u5s: Solution structures of Brd2 second bromodomain in complex with st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u5s
TitleSolution structures of Brd2 second bromodomain in complex with stat3 peptide
Components
  • Bromodomain-containing protein 2
  • Stat3 peptide
KeywordsTRANSCRIPTION / Brd2 / Brd4 / bromodomain / stat3 / th17 / p300
Function / homology
Function and homology information


PTK6 Activates STAT3 / RNA sequestering activity / eye photoreceptor cell differentiation / radial glial cell differentiation / negative regulation of primary miRNA processing / retinal rod cell differentiation / leptin-mediated signaling pathway / negative regulation of hydrogen peroxide biosynthetic process / T-helper 17 type immune response / Signalling to STAT3 ...PTK6 Activates STAT3 / RNA sequestering activity / eye photoreceptor cell differentiation / radial glial cell differentiation / negative regulation of primary miRNA processing / retinal rod cell differentiation / leptin-mediated signaling pathway / negative regulation of hydrogen peroxide biosynthetic process / T-helper 17 type immune response / Signalling to STAT3 / negative regulation of neuron migration / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of extracellular matrix disassembly / negative regulation of inflammatory response to wounding / primary miRNA binding / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / cellular response to interleukin-17 / T-helper 17 cell lineage commitment / response to leptin / regulation of feeding behavior / sexual reproduction / Interleukin-9 signaling / Interleukin-21 signaling / Transcriptional regulation of pluripotent stem cells / interleukin-9-mediated signaling pathway / nuclear glucocorticoid receptor binding / MET activates STAT3 / regulation of cellular response to hypoxia / interleukin-10-mediated signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / interleukin-2-mediated signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / acetylation-dependent protein binding / cellular response to leptin stimulus / interleukin-15-mediated signaling pathway / interleukin-23-mediated signaling pathway / postsynapse to nucleus signaling pathway / Interleukin-23 signaling / negative regulation of stem cell differentiation / astrocyte differentiation / chromatin looping / Signaling by cytosolic FGFR1 fusion mutants / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / Interleukin-37 signaling / regulation of mitochondrial membrane permeability / Signaling by Leptin / cell surface receptor signaling pathway via STAT / positive regulation of cytokine production involved in inflammatory response / Interleukin-27 signaling / Interleukin-35 Signalling / phosphorylation / negative regulation of glycolytic process / positive regulation of vascular endothelial cell proliferation / eating behavior / growth hormone receptor signaling pathway / Signaling by ALK / Interleukin-20 family signaling / Interleukin-6 signaling / temperature homeostasis / interleukin-6-mediated signaling pathway / lncRNA binding / positive regulation of Notch signaling pathway / Interleukin-10 signaling / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of ATP biosynthetic process / positive regulation of interleukin-10 production / positive regulation of vascular endothelial growth factor production / RUNX3 regulates p14-ARF / somatic stem cell population maintenance / regulation of multicellular organism growth / growth hormone receptor signaling pathway via JAK-STAT / cell surface receptor signaling pathway via JAK-STAT / positive regulation of T-helper 17 cell lineage commitment / Growth hormone receptor signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / cellular response to hormone stimulus / Nuclear events stimulated by ALK signaling in cancer / intracellular receptor signaling pathway / Signaling by CSF3 (G-CSF) / energy homeostasis / protein localization to chromatin / positive regulation of phagocytosis / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / Interleukin-7 signaling / Downstream signal transduction / : / negative regulation of autophagy / protein sequestering activity / transforming growth factor beta receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of erythrocyte differentiation / histone reader activity / positive regulation of interleukin-1 beta production / response to ischemia / acute-phase response
Similarity search - Function
STAT3, SH2 domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain ...STAT3, SH2 domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / p53-like transcription factor, DNA-binding / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / SH2 domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain (BrD) profile. / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 2 / Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZeng, L. / Zhou, M.-M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Mol. Cell / Year: 2017
Title: Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation.
Authors: Cheung, K.L. / Zhang, F. / Jaganathan, A. / Sharma, R. / Zhang, Q. / Konuma, T. / Shen, T. / Lee, J.Y. / Ren, C. / Chen, C.H. / Lu, G. / Olson, M.R. / Zhang, W. / Kaplan, M.H. / Littman, D.R. ...Authors: Cheung, K.L. / Zhang, F. / Jaganathan, A. / Sharma, R. / Zhang, Q. / Konuma, T. / Shen, T. / Lee, J.Y. / Ren, C. / Chen, C.H. / Lu, G. / Olson, M.R. / Zhang, W. / Kaplan, M.H. / Littman, D.R. / Walsh, M.J. / Xiong, H. / Zeng, L. / Zhou, M.M.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_exptl ...pdbx_audit_support / pdbx_nmr_exptl / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_exptl.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 20, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Stat3 peptide


Theoretical massNumber of molelcules
Total (without water)14,6982
Polymers14,6982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13157.136 Da / Num. of mol.: 1 / Fragment: UNP residues 344-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide Stat3 peptide


Mass: 1540.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40763*PLUS
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D HN(CA)CB
122isotropic13D HN(COCA)CB
132isotropic23D 1H-15N NOESY
141isotropic33D 1H-13C NOESY aliphatic
151isotropic33D 1H-13C NOESY aromatic
161isotropic23D 1H-13C filtered NOESY aliphatic
171isotropic23D 1H-13C filtered NOESY aromatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 100% D2Osample_1100% D2O
solution210 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
2 mMEDTAnatural abundance1
2 mMDTT[U-2H]1
10 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
2 mMEDTAnatural abundance2
2 mMDTT[U-2H]2
Sample conditionsIonic strength: null Not defined / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE9003

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
NMRView5.04Johnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxrefinement
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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