[English] 日本語
Yorodumi
- PDB-4c5h: Crystal structure of the minimal Pho-Sfmbt complex (P3121 spacegroup) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c5h
TitleCrystal structure of the minimal Pho-Sfmbt complex (P3121 spacegroup)
Components
  • POLYCOMB PROTEIN PHO
  • POLYCOMB PROTEIN SFMBT
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


Transcriptional Regulation by E2F6 / polytene chromosome puff / imaginal disc growth / DNA Damage Recognition in GG-NER / SUMOylation of chromatin organization proteins / Estrogen-dependent gene expression / UCH proteinases / polytene chromosome / PcG protein complex / Ino80 complex ...Transcriptional Regulation by E2F6 / polytene chromosome puff / imaginal disc growth / DNA Damage Recognition in GG-NER / SUMOylation of chromatin organization proteins / Estrogen-dependent gene expression / UCH proteinases / polytene chromosome / PcG protein complex / Ino80 complex / anterior/posterior axis specification / dendrite morphogenesis / oogenesis / DNA topological change / methylated histone binding / transcription initiation-coupled chromatin remodeling / chromatin DNA binding / heterochromatin formation / DNA recombination / transcription regulator complex / sequence-specific DNA binding / 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 / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / DNA binding / zinc ion binding / nucleus / metal ion binding
Similarity search - Function
Sfmbt, SAM domain / : / : / : / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Mbt repeat / MBT repeat profile. ...Sfmbt, SAM domain / : / : / : / 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 / SAM domain (Sterile alpha motif) / SH3 type barrels. - #140 / Zinc finger, C2H2 type / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / zinc finger / Sterile alpha motif/pointed domain superfamily / 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
Polycomb protein PHO / Polycomb protein Sfmbt
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 11, 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: POLYCOMB PROTEIN SFMBT
B: POLYCOMB PROTEIN PHO


Theoretical massNumber of molelcules
Total (without water)66,0872
Polymers66,0872
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-14 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.780, 120.780, 153.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein POLYCOMB PROTEIN SFMBT / SCM-LIKE WITH FOUR MBT DOMAIN-CONTAINING PROTEIN 1 / DSFMBT


Mass: 51067.664 Da / Num. of mol.: 1 / Fragment: 4MBT, RESIDUES 531-980
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9VK33
#2: Protein POLYCOMB PROTEIN PHO / PROTEIN PLEIOHOMEOTIC / TRANSCRIPTION FACTOR YY1 HOMOLOG


Mass: 15019.656 Da / Num. of mol.: 1 / Fragment: SPACER, RESIDUES 116-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q8ST83

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.88 Å3/Da / Density % sol: 80.3 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.13747
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13747 Å / Relative weight: 1
ReflectionResolution: 3.2→3.28 Å / Num. obs: 21760 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 7.7 % / Biso Wilson estimate: 85.62 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.3
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.3 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H6Z

3h6z


Resolution: 3.2→49.489 Å / SU ML: 0.49 / σ(F): 1.36 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1088 5 %
Rwork0.2208 --
obs0.2215 21757 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.2 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 0 0 3497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023743
X-RAY DIFFRACTIONf_angle_d0.6055087
X-RAY DIFFRACTIONf_dihedral_angle_d10.4571333
X-RAY DIFFRACTIONf_chiral_restr0.044538
X-RAY DIFFRACTIONf_plane_restr0.003654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.34570.41071340.3612532X-RAY DIFFRACTION99
3.3457-3.5220.32181330.30282529X-RAY DIFFRACTION100
3.522-3.74260.27581330.25682559X-RAY DIFFRACTION100
3.7426-4.03150.23091360.2082570X-RAY DIFFRACTION100
4.0315-4.4370.19491340.17732558X-RAY DIFFRACTION100
4.437-5.07840.17071370.17312590X-RAY DIFFRACTION100
5.0784-6.39610.25511370.21312613X-RAY DIFFRACTION100
6.3961-49.49450.21471440.22322718X-RAY DIFFRACTION100

+
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