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- PDB-4c5i: Crystal structure of MBTD1 YY1 complex -

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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 / histone H4K20me1 reader activity / immunoglobulin heavy chain V-D-J recombination / response to prostaglandin F / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / histone H4K20me2 reader activity / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / negative regulation of interferon-beta production ...NuA4 histone acetyltransferase complex binding / histone H4K20me1 reader activity / immunoglobulin heavy chain V-D-J recombination / response to prostaglandin F / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / histone H4K20me2 reader activity / negative regulation of cell growth involved in cardiac muscle cell development / PcG protein complex / negative regulation of interferon-beta production / Ino80 complex / chromatin silencing complex / response to UV-C / regulation of double-strand break repair / DNA-binding transcription repressor activity / SMAD binding / lncRNA binding / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of DNA replication / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / positive regulation of double-strand break repair via homologous recombination / B cell differentiation / four-way junction DNA binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of miRNA transcription / regulation of embryonic development / telomere maintenance / positive regulation of DNA repair / promoter-specific chromatin binding / double-strand break repair via homologous recombination / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA Damage Recognition in GG-NER / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / sequence-specific double-stranded DNA binding / cellular response to UV / UCH proteinases / site of double-strand break / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / histone binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / regulation of apoptotic process / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / ribonucleoprotein complex / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / RNA binding / nucleoplasm / zinc 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 ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

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

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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

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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

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