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- PDB-5wak: Crystal Structure of a Suz12-Rbbp4 Binary Complex -

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Basic information

Entry
Database: PDB / ID: 5wak
TitleCrystal Structure of a Suz12-Rbbp4 Binary Complex
Components
  • Histone-binding protein RBBP4
  • Polycomb protein SUZ12Polycomb-group proteins
KeywordsTRANSCRIPTION / Methyltransferase
Function / homology
Function and homology information


sex chromatin / CAF-1 complex / random inactivation of X chromosome / facultative heterochromatin formation / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex ...sex chromatin / CAF-1 complex / random inactivation of X chromosome / facultative heterochromatin formation / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Polo-like kinase mediated events / lncRNA binding / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / histone deacetylase complex / G0 and Early G1 / enzyme activator activity / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / methylated histone binding / Regulation of TP53 Activity through Acetylation / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / chromatin DNA binding / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / histone binding / Oxidative Stress Induced Senescence / cell population proliferation / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / nuclear body / chromatin remodeling / cell cycle / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol
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 / WD40 repeat, conserved site ...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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone-binding protein RBBP4 / Polycomb protein SUZ12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChen, S. / Jiao, L. / Liu, X.
CitationJournal: Mol. Cell / Year: 2018
Title: Unique Structural Platforms of Suz12 Dictate Distinct Classes of PRC2 for Chromatin Binding.
Authors: Chen, S. / Jiao, L. / Shubbar, M. / Yang, X. / Liu, X.
History
DepositionJun 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-binding protein RBBP4
B: Polycomb protein SUZ12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1193
Polymers105,0542
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-29 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.976, 107.696, 107.769
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 Histone-binding protein RBBP4 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 49367.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#2: Protein Polycomb protein SUZ12 / Polycomb-group proteins / Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor ...Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor of zeste 12 protein homolog


Mass: 55686.227 Da / Num. of mol.: 1 / Fragment: UNP residues 76-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15022
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% polyethylene glycol (PEG) 3350, 100 mM ammonium citrate tribasic and 100 mM Tris-HCl, pH 8.6

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→28.76 Å / Num. obs: 15396 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 52.41 Å2 / Net I/σ(I): 23.6
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.788 / Rpim(I) all: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFC

3gfc


Resolution: 3.2→28.76 Å / Cor.coef. Fo:Fc: 0.9046 / Cor.coef. Fo:Fc free: 0.8458 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.483
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 797 5.18 %RANDOM
Rwork0.1781 ---
obs0.1819 15396 73.63 %-
Displacement parametersBiso mean: 75.12 Å2
Baniso -1Baniso -2Baniso -3
1-12.5673 Å20 Å20 Å2
2---3.9185 Å20 Å2
3----8.6488 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: 1 / Resolution: 3.2→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 1 0 4766
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014886HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.256622HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1691SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes691HARMONIC5
X-RAY DIFFRACTIONt_it4886HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion23.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion633SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5540SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3061 48 4.99 %
Rwork0.1722 914 -
all0.1791 962 -
obs--25.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6089-0.16660.14246.59640.29112.38730.14620.2137-0.3913-0.5513-0.02941.03580.1976-0.4002-0.1168-0.21180.0255-0.0131-0.28120.0876-0.2331-16.6035-23.657623.1828
20.4931.149-0.66246.28220.55211.51340.3894-0.36530.38860.815-0.21280.5498-0.533-0.1641-0.17660.03140.03270.2394-0.26040.1038-0.2791-11.399-0.90836.8596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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