[English] 日本語
Yorodumi
- PDB-4u2m: Crystal structure of a complex of the Miz1- and BCL6 POZ domains. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u2m
TitleCrystal structure of a complex of the Miz1- and BCL6 POZ domains.
ComponentsZinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / POZ domain / BTB domain
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 / ectoderm development / 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 / ectoderm development / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / XBP1(S) activates chaperone genes / paraspeckles / germinal center formation / pyramidal neuron differentiation / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / gastrulation with mouth forming second / 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 / G1 to G0 transition / regulation of T cell proliferation / negative regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / regulation of cell differentiation / negative regulation of cellular senescence / Rho protein signal transduction / negative regulation of cell cycle / regulation of immune response / erythrocyte development / heterochromatin formation / core promoter sequence-specific DNA binding / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / protein-DNA complex / cell morphogenesis / protein localization / negative regulation of cell growth / chromatin DNA binding / transcription coactivator 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 cell population proliferation / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
C2H2-type zinc finger / 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. ...C2H2-type zinc finger / 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 / Zinc finger and BTB domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsStead, M.A. / Wright, S.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Yorkshire Cancer ResearchL334 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structures of heterodimeric POZ domains of Miz1/BCL6 and Miz1/NAC1.
Authors: Stead, M.A. / Wright, S.C.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
B: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
C: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
D: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)113,3114
Polymers113,3114
Non-polymers00
Water2,936163
1
A: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.850, 97.880, 119.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are four biological units in the asymmetric unit.

-
Components

#1: Protein
Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein / Myc-interacting zinc finger protein 1 / Miz-1 / Zinc finger protein 151 / Zinc finger protein 60 / ...Myc-interacting zinc finger protein 1 / Miz-1 / Zinc finger protein 151 / Zinc finger protein 60 / 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: 28327.648 Da / Num. of mol.: 4
Fragment: POZ domain, UNP residues 2-115,POZ domain, UNP residues 5-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ZBTB17, MIZ1, ZNF151, ZNF60, BCL6, BCL5, LAZ3, ZBTB27, ZNF51
Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13105, UniProt: P41182
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 4 % PEG 3350, 3 % 2-propanol, 0.2 M ammonium citrate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2014
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.23→58.47 Å / Num. obs: 52962 / % possible obs: 99.3 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.025 / Net I/σ(I): 19 / Num. measured all: 215105
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.23-2.293.90.3114.81463337380.9190.17396.2
9.97-58.473.40.02150.823046690.990.01398.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.77 Å58.47 Å
Translation5.77 Å58.47 Å

-
Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
XDSdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
ARPmodel building
REFMAC5.8.0073refinement
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→58.47 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.198 / FOM work R set: 0.8008 / SU B: 6.899 / SU ML: 0.169 / SU R Cruickshank DPI: 0.2853 / SU Rfree: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 2580 4.9 %RANDOM
Rwork0.2114 50287 --
obs0.2129 52867 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.85 Å2 / Biso mean: 46.076 Å2 / Biso min: 24.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å20 Å2
2--1.61 Å20 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 2.23→58.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7161 0 0 163 7324
Biso mean---50.29 -
Num. residues----941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197305
X-RAY DIFFRACTIONr_bond_other_d0.0080.026993
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9529912
X-RAY DIFFRACTIONr_angle_other_deg1.457315953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29724.613310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7541529
X-RAY DIFFRACTIONr_chiral_restr0.0850.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028319
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021702
X-RAY DIFFRACTIONr_mcbond_it3.9854.4873765
X-RAY DIFFRACTIONr_mcbond_other3.9824.4863764
X-RAY DIFFRACTIONr_mcangle_it5.5346.7044689
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.582 160 -
Rwork0.589 3532 -
all-3692 -
obs--95.08 %

+
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