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- PDB-4c5h: Crystal structure of the minimal Pho-Sfmbt complex (P3121 spacegroup) -

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Basic information

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


SUMOylation of chromatin organization proteins / Transcriptional Regulation by E2F6 / polytene chromosome puff / imaginal disc growth / DNA Damage Recognition in GG-NER / UCH proteinases / polytene chromosome / PcG protein complex / Ino80 complex / dendrite morphogenesis ...SUMOylation of chromatin organization proteins / Transcriptional Regulation by E2F6 / polytene chromosome puff / imaginal disc growth / DNA Damage Recognition in GG-NER / UCH proteinases / polytene chromosome / PcG protein complex / Ino80 complex / dendrite morphogenesis / anterior/posterior axis specification / oogenesis / DNA topological change / heterochromatin formation / transcription initiation-coupled chromatin remodeling / methylated histone binding / chromatin DNA binding / 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 / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / metal ion binding / nucleus
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 / zinc finger / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Sterile alpha motif/pointed domain 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYCOMB PROTEIN SFMBT
B: POLYCOMB PROTEIN PHO


Theoretical massNumber of molelcules
Total (without water)66,0872
Polymers66,0872
Non-polymers00
Water0
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

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Components

#1: Protein POLYCOMB PROTEIN SFMBT / Polycomb-group proteins / 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 / Polycomb-group proteins / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

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

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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

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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

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