[English] 日本語
Yorodumi
- PDB-4c5i: Crystal structure of MBTD1 YY1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c5i
TitleCrystal structure of MBTD1 YY1 complex
Components
  • MBT DOMAIN-CONTAINING PROTEIN 1
  • TRANSCRIPTIONAL REPRESSOR PROTEIN YY1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


NuA4 histone acetyltransferase complex binding / response to prostaglandin F / RNA localization / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / embryonic skeletal system development / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / camera-type eye morphogenesis / regulation of double-strand break repair ...NuA4 histone acetyltransferase complex binding / response to prostaglandin F / RNA localization / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / embryonic skeletal system development / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / camera-type eye morphogenesis / regulation of double-strand break repair / Ino80 complex / chromatin silencing complex / negative regulation of interferon-beta production / response to UV-C / NuA4 histone acetyltransferase complex / anterior/posterior pattern specification / regulation of chromosome organization / DNA-binding transcription repressor activity / immunoglobulin heavy chain V-D-J recombination / positive regulation of double-strand break repair via homologous recombination / SMAD binding / regulation of DNA replication / regulation of embryonic development / regulation of DNA repair / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / four-way junction DNA binding / methylated histone binding / positive regulation of DNA repair / telomere maintenance / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / B cell differentiation / negative regulation of miRNA transcription / double-strand break repair via homologous recombination / DNA Damage Recognition in GG-NER / nuclear matrix / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / cellular response to UV / nucleosome / sequence-specific double-stranded DNA binding / site of double-strand break / chromatin organization / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
C2H2-type Zinc finger protein, YY1-like / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 ...C2H2-type Zinc finger protein, YY1-like / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Transcriptional repressor protein YY1 / MBT domain-containing protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.586 Å
AuthorsAlfieri, C. / Glatt, S. / Mueller, C.W.
CitationJournal: Genes Dev. / Year: 2013
Title: Structural Basis for Targeting the Chromatin Repressor Sfmbt to Polycomb Response Elements
Authors: Alfieri, C. / Gambetta, M.C. / Matos, R. / Glatt, S. / Sehr, P. / Fraterman, S. / Wilm, M. / Mueller, J. / Mueller, C.W.
History
DepositionSep 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MBT DOMAIN-CONTAINING PROTEIN 1
B: MBT DOMAIN-CONTAINING PROTEIN 1
C: TRANSCRIPTIONAL REPRESSOR PROTEIN YY1


Theoretical massNumber of molelcules
Total (without water)103,1803
Polymers103,1803
Non-polymers00
Water1,58588
1
A: MBT DOMAIN-CONTAINING PROTEIN 1
C: TRANSCRIPTIONAL REPRESSOR PROTEIN YY1


Theoretical massNumber of molelcules
Total (without water)53,3552
Polymers53,3552
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-14.3 kcal/mol
Surface area22260 Å2
MethodPISA
2
B: MBT DOMAIN-CONTAINING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)49,8251
Polymers49,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.360, 104.710, 135.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MBT DOMAIN-CONTAINING PROTEIN 1 / MBTD1


Mass: 49825.051 Da / Num. of mol.: 2 / Fragment: 4MBT, RESIDUES 130-566
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q05BQ5
#2: Protein/peptide TRANSCRIPTIONAL REPRESSOR PROTEIN YY1 / DELTA TRANSCRIPTION FACTOR / INO80 COMPLEX SUBUNIT S / NF-E1 / YIN AND YANG 1 / YY-1 / YY1


Mass: 3529.880 Da / Num. of mol.: 1 / Fragment: SPACER, RESIDUES 199-228 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P25490
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 52.4 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93432
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93432 Å / Relative weight: 1
ReflectionResolution: 2.6→2.65 Å / Num. obs: 31789 / % possible obs: 99.2 % / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.5 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FEO

3feo


Resolution: 2.586→48.807 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 1589 5 %
Rwork0.2129 --
obs0.214 31775 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.586→48.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6816 0 0 88 6904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037025
X-RAY DIFFRACTIONf_angle_d0.6329548
X-RAY DIFFRACTIONf_dihedral_angle_d11.1892529
X-RAY DIFFRACTIONf_chiral_restr0.0451010
X-RAY DIFFRACTIONf_plane_restr0.0031222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5861-2.66960.39611400.32182663X-RAY DIFFRACTION98
2.6696-2.7650.31881440.30192720X-RAY DIFFRACTION100
2.765-2.87570.30831420.27672713X-RAY DIFFRACTION100
2.8757-3.00650.27671430.26562722X-RAY DIFFRACTION100
3.0065-3.1650.30751430.25042726X-RAY DIFFRACTION100
3.165-3.36330.24991450.23152751X-RAY DIFFRACTION100
3.3633-3.62290.23711440.20652732X-RAY DIFFRACTION100
3.6229-3.98730.21411450.19292747X-RAY DIFFRACTION100
3.9873-4.56390.21661440.172742X-RAY DIFFRACTION99
4.5639-5.74860.1731480.17532810X-RAY DIFFRACTION99
5.7486-48.81550.1791510.19172860X-RAY DIFFRACTION97

+
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