[English] 日本語
Yorodumi
- PDB-3e4u: Crystal Structure of the Wild-Type Human BCL6 BTB/POZ Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e4u
TitleCrystal Structure of the Wild-Type Human BCL6 BTB/POZ Domain
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / BTB/POZ Protein Interaction Domain / Activator / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Proto-oncogene / Repressor / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


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 mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation ...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 mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation / paraspeckles / germinal center formation / pyramidal neuron differentiation / type 2 immune response / regulation of immune system process / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of cell differentiation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / heterochromatin formation / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / cell morphogenesis / protein localization / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / 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 / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsStead, M.A. / Rosbrook, G.O. / Hadden, J.M. / Trinh, C.H. / Carr, S.B. / Wright, S.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of the wild-type human BCL6 POZ domain.
Authors: Stead, M.A. / Rosbrook, G.O. / Hadden, J.M. / Trinh, C.H. / Carr, S.B. / Wright, S.C.
History
DepositionAug 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
C: B-cell lymphoma 6 protein
D: B-cell lymphoma 6 protein
E: B-cell lymphoma 6 protein
F: B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)88,4236
Polymers88,4236
Non-polymers00
Water4,612256
1
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-32 kcal/mol
Surface area12590 Å2
MethodPISA
2
C: B-cell lymphoma 6 protein
D: B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-32 kcal/mol
Surface area12610 Å2
MethodPISA
3
E: B-cell lymphoma 6 protein
F: B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)29,4742
Polymers29,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-28 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.209, 59.209, 158.971
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

-
Components

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


Mass: 14737.150 Da / Num. of mol.: 6 / Fragment: BTB Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P41182
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 1.82 Å3/Da / Density % sol: 32.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.5 M sodium nitrate, 100 mM sodium acetate (pH 4.5), 40 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2008 / Details: mirrors
RadiationMonochromator: Sagitally focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.1→36.86 Å / Num. obs: 36195 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 31.082 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.6 / Num. measured all: 20521 / Num. unique all: 5312 / Rsym value: 0.157 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.399 / Cor.coef. Fo:Fc: 0.59 / Cor.coef. Io to Ic: 0.595

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.86 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.275 / WRfactor Rwork: 0.24 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.826 / SU R Cruickshank DPI: 0.072 / SU Rfree: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1887 5.2 %RANDOM
Rwork0.219 ---
all0.221 36419 --
obs0.221 36147 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.86 Å2 / Biso mean: 33.169 Å2 / Biso min: 12.22 Å2
Baniso -1Baniso -2Baniso -3
1-11.16 Å20 Å20 Å2
2--11.16 Å20 Å2
3----22.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5571 0 0 256 5827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225631
X-RAY DIFFRACTIONr_bond_other_d00.023789
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9597569
X-RAY DIFFRACTIONr_angle_other_deg4.23739201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61223.176255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.938151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6391549
X-RAY DIFFRACTIONr_chiral_restr0.0690.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026041
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021176
X-RAY DIFFRACTIONr_mcbond_it0.5911.53456
X-RAY DIFFRACTIONr_mcbond_other01.51403
X-RAY DIFFRACTIONr_mcangle_it1.05125593
X-RAY DIFFRACTIONr_scbond_it1.54732175
X-RAY DIFFRACTIONr_scangle_it2.2424.51976
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 124 -
Rwork0.152 2558 -
all-2682 -
obs-2558 99.96 %

+
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://pdbjlvh1.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