[English] 日本語
Yorodumi
- PDB-6xxs: Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xxs
TitleCrystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with the NcoR1 BBD1 corepressor peptide.
Components
  • (B-cell lymphoma 6 protein) x 2
  • Nuclear receptor corepressor 1
KeywordsTRANSCRIPTION / BCL6 / NCoR1.
Function / homology
Function and homology information


NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 androgen receptor signaling pathway ...NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 androgen receptor signaling pathway / 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 / pyramidal neuron differentiation / type 2 immune response / negative regulation of JNK cascade / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / negative regulation of glycolytic process / positive regulation of cell motility / nuclear thyroid hormone receptor binding / FOXO-mediated transcription of cell death genes / negative regulation of Rho protein signal transduction / negative regulation of cell-matrix adhesion / negative regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / regulation of T cell proliferation / regulation of cell differentiation / negative regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / Notch-HLH transcription pathway / B cell proliferation / locomotor rhythm / negative regulation of cellular senescence / histone deacetylase complex / Rho protein signal transduction / Regulation of MECP2 expression and activity / regulation of immune response / spindle assembly / erythrocyte development / Nuclear signaling by ERBB4 / positive regulation of B cell proliferation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of cytokine production / transcription repressor complex / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cell-matrix adhesion / transcription corepressor binding / negative regulation of miRNA transcription / cell motility / nuclear receptor binding / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / negative regulation of cell growth / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / heterochromatin formation / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / sequence-specific double-stranded DNA binding / protein localization / Circadian Clock / chromatin organization / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / inflammatory response / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / 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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Homeobox-like domain superfamily
Similarity search - Domain/homology
Nuclear receptor corepressor 1 / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsZacharchenko, T. / Wright, S.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Kay Kendall Leukaemia FundKKLF1047 United Kingdom
CitationJournal: Iucrj / Year: 2021
Title: Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone.
Authors: Zacharchenko, T. / Wright, S.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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 corepressor 1
D: Nuclear receptor corepressor 1
E: B-cell lymphoma 6 protein
G: Nuclear receptor corepressor 1
F: B-cell lymphoma 6 protein
H: Nuclear receptor corepressor 1


Theoretical massNumber of molelcules
Total (without water)68,7358
Polymers68,7358
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19840 Å2
ΔGint-110 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.380, 165.380, 244.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

-
Components

#1: Protein B-cell lymphoma 6 protein / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing ...BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing protein 27 / Zinc finger protein 51


Mass: 15488.877 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182
#2: Protein/peptide
Nuclear receptor corepressor 1 / N-CoR1


Mass: 1942.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75376
#3: Protein B-cell lymphoma 6 protein / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing ...BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing protein 27 / Zinc finger protein 51


Mass: 14498.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 7.14 Å3/Da / Density % sol: 82.76 %
Description: Rod like crystals, High-Solvent content, Porous lattice.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2M Sodium chloride 5%(w/v) PEG 4000 0.1M Tris base/ Hydrochloric acid pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.25→93.05 Å / Num. obs: 31807 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 72.67 Å2 / CC1/2: 0.958 / Rpim(I) all: 0.17 / Net I/σ(I): 5.5
Reflection shellResolution: 3.25→3.43 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4532 / CC1/2: 0.154 / Rpim(I) all: 0.818 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R28

1r28


Resolution: 3.25→82.69 Å / SU ML: 0.4326 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1610 5.07 %
Rwork0.1966 30166 -
obs0.198 31776 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.26 Å2
Refinement stepCycle: LAST / Resolution: 3.25→82.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 0 0 4675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354764
X-RAY DIFFRACTIONf_angle_d0.5756425
X-RAY DIFFRACTIONf_chiral_restr0.0463756
X-RAY DIFFRACTIONf_plane_restr0.0036819
X-RAY DIFFRACTIONf_dihedral_angle_d16.96091827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.350.35741180.34042447X-RAY DIFFRACTION99.65
3.35-3.450.33441340.32442470X-RAY DIFFRACTION100
3.45-3.580.31671260.30422459X-RAY DIFFRACTION100
3.58-3.720.28171330.2622470X-RAY DIFFRACTION99.96
3.72-3.890.2671260.22392495X-RAY DIFFRACTION100
3.89-4.090.2611450.20552468X-RAY DIFFRACTION100
4.09-4.350.19121440.16412493X-RAY DIFFRACTION100
4.35-4.690.14771380.13472492X-RAY DIFFRACTION100
4.69-5.160.15131390.13152511X-RAY DIFFRACTION99.96
5.16-5.90.23591310.16062548X-RAY DIFFRACTION99.96
5.91-7.440.19741120.19592594X-RAY DIFFRACTION99.96
7.44-82.690.20881640.16862719X-RAY DIFFRACTION99.41
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.962886733621.218885072031.632337128052.524398373910.5455193699072.628297285650.07611558202610.212854920273-0.130213666916-0.02570743023980.1669448470190.01172054046910.294397479286-0.109407784955-0.2496779248810.3754215022710.0203816435334-0.0006341447919970.48608535318-0.05243914011620.340176737173-71.548547871236.3347285051-46.6411398856
21.871214729330.08465539513150.7578130036681.575469562951.133453981395.549796126460.0831073649958-0.2380611799940.2079101596180.256868477663-0.0371700236749-0.160384563480.147771595029-0.121880584939-0.04520666751610.418309319531-0.0473954545934-0.02142750177520.419850935569-0.04133255929190.401718770688-62.28561934144.4822243587-34.8781383309
37.67281203209-0.217739987561-1.452326983015.773270515071.897446497595.93077979736-0.2139409890470.2216522832591.12673486071-0.177274972190.739156554975-0.272711825672-0.273767456245-0.268264030588-0.6022343476640.6435048886860.0069671414204-0.0265649122120.4255260997940.01339848947370.291737210891-68.835268482543.8845163879-54.1517529994
44.9064989564-0.0627577077280.9926010671615.159955695950.9130011171374.31910370410.03061980126350.3157114008060.125307114795-0.781301269960.203963985741-0.721586083028-0.02505943690821.19893807225-0.4167697448870.420830018314-0.110857181820.01384129152620.486139542284-0.1905792657250.534241143738-53.437811971144.1675969014-40.9787763971
56.314043135630.7153262479080.539760610233.580234425930.6622597385671.931927347980.02965359366660.0412954104513-0.08302743075140.2759042759690.102374539429-0.2028080098620.1284812086480.290356887723-0.1010146548560.5490154565740.049683593035-0.10507468470.393013358752-0.09018662428090.420243791781-63.4960866701-1.95668451533-57.5348669913
63.83644561357-3.044512845334.007944118864.18652814051-6.043888608288.794264643270.4434404566180.495581769776-0.7174628098521.02252815910.305757392118-0.328806018357-0.7605228886751.27985328908-0.7993002093280.8161653781250.03246911603230.01933532040790.594425577379-0.3688543183060.981740808421-52.2329968967-6.64005735831-59.6485386247
71.434064496541.185610053920.1633915358872.69720105817-0.03827046780111.40282245702-0.224853162440.1244049761430.1120367222920.01388436002930.426605612681-0.982542874481-0.09939948522430.52000189915-0.1654376371940.476375169156-0.0187388568982-0.0568993674280.692925148897-0.2418800088440.751151831184-51.229116308913.7269756445-53.8391749044
88.03836120552-5.45478686177-5.066031852074.22763331283.529691948213.29283820449-0.6294368043630.8603998468380.1664553164010.7099623729440.606039659738-0.9931994594011.28688953121-0.08254815985310.2526776149150.6851733247330.102062686088-0.1426001035181.06733996271-0.2965410825541.00831452074-44.44993727357.71544742814-47.2678548684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -2 through 127)
2X-RAY DIFFRACTION2(chain 'B' and resid -4 through 126)
3X-RAY DIFFRACTION3(chain 'C' and resid 1340 through 1356)
4X-RAY DIFFRACTION4(chain 'D' and resid 1341 through 1356)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 127)
6X-RAY DIFFRACTION6(chain 'G' and resid 1340 through 1356)
7X-RAY DIFFRACTION7(chain 'F' and resid -2 through 126)
8X-RAY DIFFRACTION8(chain 'H' and resid 1341 through 1356)

+
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