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- PDB-2yb8: Crystal structure of Nurf55 in complex with Su(z)12 -

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Basic information

Entry
Database: PDB / ID: 2yb8
TitleCrystal structure of Nurf55 in complex with Su(z)12
Components
  • POLYCOMB PROTEIN SU(Z)12
  • PROBABLE HISTONE-BINDING PROTEIN CAF1
KeywordsTRANSCRIPTION / HISTONE METHLYATION / CHROMATIN REMODELLING / P55 / RBBP4 / RBBP7 / RBAP46 / RBAP48 / PRC2 / H4 / H3K27 / H3K4 / WD40 DOMAIN
Function / homology
Function and homology information


negative regulation of response to gamma radiation / : / : / G0 and Early G1 / Regulation of TP53 Activity through Acetylation / : / Transcriptional Regulation by E2F6 / : / Regulation of PTEN gene transcription / Neddylation ...negative regulation of response to gamma radiation / : / : / G0 and Early G1 / Regulation of TP53 Activity through Acetylation / : / Transcriptional Regulation by E2F6 / : / Regulation of PTEN gene transcription / Neddylation / eggshell chorion gene amplification / PRC2 methylates histones and DNA / HDACs deacetylate histones / HATs acetylate histones / Myb complex / Oxidative Stress Induced Senescence / segment specification / CAF-1 complex / polytene chromosome / facultative heterochromatin formation / chromatin => GO:0000785 / NURF complex / NuRD complex / nucleosome organization / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / histone methyltransferase complex / Sin3-type complex / regulation of mitotic cell cycle / neurogenesis / heterochromatin formation / chromatin DNA binding / histone deacetylase binding / chromatin organization / histone binding / transcription regulator complex / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus / metal ion binding
Similarity search - Function
Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 type domain signature. / G-protein beta WD-40 repeat ...Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 type domain signature. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chromatin assembly factor 1 p55 subunit / Polycomb protein Su(z)12
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. ...Schmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. / Bunker, R.D. / Wirth, U. / Bouwmeester, T. / Bauer, A. / Ly-Hartig, N. / Zhao, K. / Chan, H. / Gu, J. / Gut, H. / Fischle, W. / Muller, J. / Thoma, N.H.
CitationJournal: Mol.Cell / Year: 2011
Title: Histone Methylation by Prc2 is Inhibited by Active Chromatin Marks.
Authors: Schmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. / Bunker, R.D. / Wirth, U. / Bouwmeester, T. / Bauer, A. / ...Authors: Schmitges, F.W. / Prusty, A.B. / Faty, M. / Stutzer, A. / Lingaraju, G.M. / Aiwazian, J. / Sack, R. / Hess, D. / Li, L. / Zhou, S. / Bunker, R.D. / Wirth, U. / Bouwmeester, T. / Bauer, A. / Ly-Hartig, N. / Zhao, K. / Chan, H. / Gu, J. / Gut, H. / Fischle, W. / Muller, J. / Thoma, N.H.
History
DepositionMar 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYCOMB PROTEIN SU(Z)12
B: PROBABLE HISTONE-BINDING PROTEIN CAF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6495
Polymers49,3612
Non-polymers2883
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-49.6 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.031, 87.189, 99.539
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/peptide POLYCOMB PROTEIN SU(Z)12 / SUPPRESSOR 12 OF ZESTE PROTEIN / SUZ12


Mass: 1598.907 Da / Num. of mol.: 1 / Fragment: NURF55 BINDING EPITOPE, RESIDUES 79-91
Source method: isolated from a genetically manipulated source
Details: PRODUCT OF SUBTILIN PROTEOLYSIS / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9NJG9
#2: Protein PROBABLE HISTONE-BINDING PROTEIN CAF1 / CHROMATIN ASSEMBLY FACTOR 1 P55 SUBUNIT / CAF-1 P55 SUBUNIT / NUCLEOSOME-REMODELING FACTOR 55 KDA ...CHROMATIN ASSEMBLY FACTOR 1 P55 SUBUNIT / CAF-1 P55 SUBUNIT / NUCLEOSOME-REMODELING FACTOR 55 KDA SUBUNIT / NURF-55 / DCAF-1 / NURF55


Mass: 47761.629 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q24572
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSTARTING MATERIAL FOR CRYSTALLIZATION INCLUDED RESIDUES 64-359 OF SU(Z)12 BEFORE PROTEOLYSIS BUT ...STARTING MATERIAL FOR CRYSTALLIZATION INCLUDED RESIDUES 64-359 OF SU(Z)12 BEFORE PROTEOLYSIS BUT PROTEIN WAS TREATED WITH 0.01 PERCENT SUBTILISIN PRIOR TO CRYSTALLIZATION. THUS MOST OF SUZ12 IS NOT PRESENT IN THE CRYSTAL STRUCTURE.

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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: 2.33 Å3/Da / Density % sol: 46.3 % / Description: NONE
Crystal growDetails: 100 MM POTASSIUM ACETATE, 2.1 M AMMONIUM SULFATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00069
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00069 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 20984 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 15.6 % / Biso Wilson estimate: 40.04 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 43.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.2 / % possible all: 92

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.58 Å / Cor.coef. Fo:Fc: 0.9498 / Cor.coef. Fo:Fc free: 0.9431 / SU R Cruickshank DPI: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.265 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.179
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 1073 5.11 %RANDOM
Rwork0.1735 ---
obs0.1748 20982 99.34 %-
Displacement parametersBiso mean: 33.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.6104 Å20 Å20 Å2
2--0.5477 Å20 Å2
3----1.1581 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 15 144 3231
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093167HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114327HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1417SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes449HARMONIC5
X-RAY DIFFRACTIONt_it3167HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion2.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3564SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.41 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2182 152 5.76 %
Rwork0.189 2485 -
all0.1906 2637 -
obs--99.34 %

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