[English] 日本語
Yorodumi
- PDB-1r2b: Crystal structure of the BCL6 BTB domain complexed with a SMRT co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r2b
TitleCrystal structure of the BCL6 BTB domain complexed with a SMRT co-repressor peptide
Components
  • B-cell lymphoma 6 protein
  • Nuclear receptor co-repressor 2
KeywordsTRANSCRIPTION / BTB domain / HDAC complex / B-cell lymphoma / transcriptional repression
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation ...Loss of MECP2 binding ability to the NCoR/SMRT complex / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / Notch binding / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / regulation of cell differentiation / regulation of T cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / Regulation of MECP2 expression and activity / negative regulation of cellular senescence / negative regulation of cell-matrix adhesion / negative regulation of Notch signaling pathway / Rho protein signal transduction / regulation of immune response / erythrocyte development / nuclear retinoid X receptor binding / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of B cell proliferation / lactation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / positive regulation of neuron differentiation / cerebellum development / regulation of cytokine production / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / enzyme activator activity / cell-matrix adhesion / transcription corepressor binding / HDACs deacetylate histones / cell motility / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PPARA activates gene expression / negative regulation of cell growth / cell morphogenesis / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / nuclear matrix / HCMV Early Events / transcription corepressor activity / sequence-specific double-stranded DNA binding / intracellular protein localization / heterochromatin formation / response to estradiol / regulation of cell population proliferation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / spermatogenesis / sequence-specific DNA binding / transcription by RNA polymerase II / nuclear body / positive regulation of apoptotic process / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / DNA binding
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / BTB/POZ domain ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Zinc finger, C2H2 type / SANT/Myb domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / Homeobox-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
B-cell lymphoma 6 protein / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAhmad, K.F. / Melnick, A. / Lax, S.A. / Bouchard, D. / Liu, J. / Kiang, C.L. / Mayer, S. / Licht, J.D. / Prive, G.G.
CitationJournal: Mol.Cell / Year: 2003
Title: Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain.
Authors: Ahmad, K.F. / Melnick, A. / Lax, S. / Bouchard, D. / Liu, J. / Kiang, C.L. / Mayer, S. / Takahashi, S. / Licht, J.D. / Prive, G.G.
History
DepositionSep 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
C: Nuclear receptor co-repressor 2
D: Nuclear receptor co-repressor 2


Theoretical massNumber of molelcules
Total (without water)33,1684
Polymers33,1684
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-45 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.228, 38.543, 76.659
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein B-cell lymphoma 6 protein / BCL-6 / Zinc finger protein 51 / LAZ-3 protein / POZ domain / BTB/POZ domain


Mass: 14559.823 Da / Num. of mol.: 2 / Fragment: BCL6 (residues 5-129) / Mutation: C8Q, C67R, C84N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6 / Plasmid: pET-32(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41182
#2: Protein/peptide Nuclear receptor co-repressor 2 / N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / SMRTe / Thyroid- ...N-CoR2 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / SMRTe / Thyroid- / retinoic-acid-receptor-associated co-repressor / T3 receptor- associating factor / TRAC / CTG repeat protein 26


Mass: 2024.325 Da / Num. of mol.: 2 / Fragment: SMRT - BBD (residues 1414-1430)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOR2 OR CTG26 / Plasmid: pET-32(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y618
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
225 %PEG33501reservoir
30.2 Mammonium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2001 / Details: Osmic confocal
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 16537 / Num. obs: 16405 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.05 / Net I/σ(I): 24
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.256 / % possible all: 92.1
Reflection
*PLUS
Highest resolution: 2.2 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 92.1 % / Rmerge(I) obs: 0.256

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→27.08 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 768 -random
Rwork0.227 ---
all0.239 16418 --
obs0.227 15876 96.7 %-
Solvent computationBsol: 37.3735 Å2 / ksol: 0.309108 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.697 Å20 Å2-0.445 Å2
2---5.141 Å20 Å2
3---4.444 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 0 130 2405
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.4831.5
X-RAY DIFFRACTIONc_mcangle_it2.4242
X-RAY DIFFRACTIONc_scbond_it2.1332
X-RAY DIFFRACTIONc_scangle_it3.0872.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.039
RfactorNum. reflection% reflection
Rfree0.399 104 -
Rwork0.298 --
obs-2378 89.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2677 / Rfactor Rwork: 0.2266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å

+
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