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- PDB-5j8y: Crystal structure of the Scm-SAM and Sfmbt-SAM heterodimer -

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Basic information

Entry
Database: PDB / ID: 5j8y
TitleCrystal structure of the Scm-SAM and Sfmbt-SAM heterodimer
Components
  • Polycomb protein ScmPolycomb-group proteins
  • Polycomb protein SfmbtPolycomb-group proteins
KeywordsNUCLEAR PROTEIN / PRC1 PhoRC SAM domain Polycom Response Element / Drosophila / signaling protein
Function / homology
Function and homology information


PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / imaginal disc growth / follicle cell of egg chamber stalk formation ...PRC1 complex binding / germarium-derived female germ-line cyst encapsulation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / imaginal disc growth / follicle cell of egg chamber stalk formation / SUMOylation of chromatin organization proteins / compound eye development / Oxidative Stress Induced Senescence / ventral cord development / polytene chromosome / negative regulation of growth / PcG protein complex / anterior/posterior axis specification / oogenesis / heterochromatin formation / methylated histone binding / axonogenesis / neurogenesis / histone binding / sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Sfmbt, SAM domain / : / : / : / Zinc finger, MYM-type / MYM-type Zinc finger with FCS sequence motif / : / Zinc finger, FCS-type / SLED domain / SLED domain superfamily ...Sfmbt, SAM domain / : / : / : / Zinc finger, MYM-type / MYM-type Zinc finger with FCS sequence motif / : / Zinc finger, FCS-type / SLED domain / SLED domain superfamily / SLED domain / 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 / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polycomb protein Scm / Polycomb protein Sfmbt
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsFrey, F. / Benda, C. / Mueller, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB1064 Germany
European Union277899 Germany
CitationJournal: Genes Dev. / Year: 2016
Title: Molecular basis of PRC1 targeting to Polycomb response elements by PhoRC.
Authors: Frey, F. / Sheahan, T. / Finkl, K. / Stoehr, G. / Mann, M. / Benda, C. / Muller, J.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein Scm
B: Polycomb protein Scm
C: Polycomb protein Sfmbt
D: Polycomb protein Sfmbt


Theoretical massNumber of molelcules
Total (without water)38,0844
Polymers38,0844
Non-polymers00
Water2,792155
1
A: Polycomb protein Scm
C: Polycomb protein Sfmbt


Theoretical massNumber of molelcules
Total (without water)19,0422
Polymers19,0422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area8500 Å2
MethodPISA
2
B: Polycomb protein Scm
D: Polycomb protein Sfmbt


Theoretical massNumber of molelcules
Total (without water)19,0422
Polymers19,0422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.956, 53.970, 61.455
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polycomb protein Scm / Polycomb-group proteins / Sex comb on midleg protein


Mass: 9054.437 Da / Num. of mol.: 2 / Fragment: UNP residues 803-877 / Mutation: L855E, L859E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Scm, CG9495 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9VHA0
#2: Protein Polycomb protein Sfmbt / Polycomb-group proteins / Scm-like with four MBT domain-containing protein 1 / dSfmbt


Mass: 9987.613 Da / Num. of mol.: 2 / Fragment: UNP residues 1137-1220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sfmbt, CG16975 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9VK33
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M Tris/HCl pH 7.5, 4% MPD, 0.2M ammonium acetate, 32.5% PEG3350
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→47.17 Å / Num. obs: 21180 / % possible obs: 96.93 % / Redundancy: 9.1 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.21
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 6.99 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.91 / % possible all: 83.18

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Processing

Software
NameVersionClassification
PHENIX1.9_1678refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pk1

1pk1


Resolution: 1.98→47.17 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.37
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 2049 5.01 %random
Rwork0.2546 ---
obs0.2558 21180 96.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 0 155 2489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032356
X-RAY DIFFRACTIONf_angle_d0.7063172
X-RAY DIFFRACTIONf_dihedral_angle_d12.287904
X-RAY DIFFRACTIONf_chiral_restr0.026365
X-RAY DIFFRACTIONf_plane_restr0.004405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9745-2.02050.4431950.43551792X-RAY DIFFRACTION68
2.0205-2.0710.39611400.34692660X-RAY DIFFRACTION97
2.071-2.1270.31971380.30482595X-RAY DIFFRACTION97
2.127-2.18960.30161370.30072633X-RAY DIFFRACTION97
2.1896-2.26020.31321380.27862641X-RAY DIFFRACTION98
2.2602-2.3410.26871400.26962649X-RAY DIFFRACTION97
2.341-2.43470.29751370.27872623X-RAY DIFFRACTION98
2.4347-2.54550.34661370.27392608X-RAY DIFFRACTION98
2.5455-2.67970.28751420.262668X-RAY DIFFRACTION98
2.6797-2.84760.27451430.26272675X-RAY DIFFRACTION98
2.8476-3.06740.26221400.26672661X-RAY DIFFRACTION99
3.0674-3.37610.29751400.24442655X-RAY DIFFRACTION98
3.3761-3.86440.24691420.2212660X-RAY DIFFRACTION99
3.8644-4.86790.23511390.20622658X-RAY DIFFRACTION99
4.8679-47.18470.23181410.23662655X-RAY DIFFRACTION99

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