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- PDB-6nq3: Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric ... -

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Basic information

Entry
Database: PDB / ID: 6nq3
TitleCrystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex
Components
  • Histone-binding protein RBBP4
  • PHD finger protein 19
  • Polycomb protein SUZ12
  • Protein Jumonji
KeywordsTRANSCRIPTION / Methyltransferase
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / sex chromatin / CAF-1 complex / random inactivation of X chromosome / ubiquitin-modified histone reader activity / facultative heterochromatin formation / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / NURF complex ...protein localization to pericentric heterochromatin / sex chromatin / CAF-1 complex / random inactivation of X chromosome / ubiquitin-modified histone reader activity / facultative heterochromatin formation / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / chromatin silencing complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / NuRD complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by DREAM complex / RSC-type complex / Polo-like kinase mediated events / lncRNA binding / cardiac muscle cell proliferation / histone methyltransferase complex / negative regulation of gene expression, epigenetic / stem cell population maintenance / Sin3-type complex / positive regulation of stem cell population maintenance / histone methyltransferase activity / G1/S-Specific Transcription / ATPase complex / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / nucleosome binding / Deposition of new CENPA-containing nucleosomes at the centromere / spleen development / enzyme activator activity / Regulation of TP53 Activity through Acetylation / methylated histone binding / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / thymus development / liver development / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / ubiquitin binding / Defective pyroptosis / cellular response to leukemia inhibitory factor / central nervous system development / HDACs deacetylate histones / stem cell differentiation / promoter-specific chromatin binding / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / chromatin DNA binding / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / Oxidative Stress Induced Senescence / DNA replication / cell population proliferation / Potential therapeutics for SARS / chromosome, telomeric region / nuclear body / chromatin remodeling / ribonucleoprotein complex / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
PHF19, PHD domain 2 / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / 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 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain ...PHF19, PHD domain 2 / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / 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 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / Tudor domain / Tudor domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / YVTN repeat-like/Quinoprotein amine dehydrogenase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / 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
Histone-binding protein RBBP4 / Polycomb protein SUZ12 / PHD finger protein 19 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.89 Å
AuthorsChen, S. / Jiao, L. / Liu, X.
CitationJournal: Mol.Cell / Year: 2020
Title: A Dimeric Structural Scaffold for PRC2-PCL Targeting to CpG Island Chromatin.
Authors: Chen, S. / Jiao, L. / Liu, X. / Yang, X. / Liu, X.
History
DepositionJan 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-binding protein RBBP4
B: Polycomb protein SUZ12
C: PHD finger protein 19
D: Protein Jumonji
E: Histone-binding protein RBBP4
F: Polycomb protein SUZ12
G: PHD finger protein 19
H: Protein Jumonji
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,93910
Polymers232,8088
Non-polymers1312
Water00
1
A: Histone-binding protein RBBP4
B: Polycomb protein SUZ12
C: PHD finger protein 19
D: Protein Jumonji
hetero molecules

A: Histone-binding protein RBBP4
B: Polycomb protein SUZ12
C: PHD finger protein 19
D: Protein Jumonji
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,93910
Polymers232,8088
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area32520 Å2
ΔGint-106 kcal/mol
Surface area63830 Å2
MethodPISA
2
E: Histone-binding protein RBBP4
F: Polycomb protein SUZ12
G: PHD finger protein 19
H: Protein Jumonji
hetero molecules

E: Histone-binding protein RBBP4
F: Polycomb protein SUZ12
G: PHD finger protein 19
H: Protein Jumonji
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,93910
Polymers232,8088
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area31560 Å2
ΔGint-118 kcal/mol
Surface area62860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.710, 139.600, 268.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 2
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 / 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.: 2
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: Protein PHD finger protein 19 / Polycomb-like protein 3 / hPCL3


Mass: 9092.757 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF19, PCL3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T6S3
#4: Protein/peptide Protein Jumonji / Jumonji/ARID domain-containing protein 2


Mass: 2257.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92833
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% polyethylene glycol (PEG) 3350, 0.1M Sodium Malonate, pH6.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.89→47.11 Å / Num. obs: 52773 / % possible obs: 98.9 % / Redundancy: 8 % / Biso Wilson estimate: 63.48 Å2 / Net I/σ(I): 17.3
Reflection shellResolution: 2.89→2.95 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.89→46.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.356
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2180 4.95 %RANDOM
Rwork0.17 ---
obs0.173 44020 82 %-
Displacement parametersBiso mean: 67.01 Å2
Baniso -1Baniso -2Baniso -3
1--7.1962 Å20 Å20 Å2
2---1.3675 Å20 Å2
3---8.5637 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.89→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11926 0 2 0 11928
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112213HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.216530HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4228SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2032HARMONIC5
X-RAY DIFFRACTIONt_it12213HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion22.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1579SEMIHARMONIC5
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_contact13510SEMIHARMONIC4
LS refinement shellResolution: 2.89→2.96 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3594 -4.43 %
Rwork0.2243 842 -
all0.23 881 -
obs--24.41 %
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)
12.77720.67780.45132.4380.05412.90030.05570.0617-0.0086-0.04470.0573-0.1541-0.37840.4948-0.113-0.2167-0.14970.0804-0.127-0.0389-0.135915.1714-23.0585-15.7392
200.4250.0351.32680.53050-0.1130.0866-0.112-0.31730.03870.25180.0312-0.20150.0743-0.08280.0413-0.08010.18620.0793-0.0002-7.3049-9.0675-20.8161
34.2060.04711.92071.6911-0.54825.29020.5075-1.0885-0.03880.1195-0.56040.3307-0.1812-0.12420.0529-0.2986-0.27180.12860.22270.065-0.1283-13.9687-33.97355.16
40.23891.4703-5.25615.00531.4521.71390.082-0.01910.4619-0.1095-0.05490.1848-0.2025-0.1928-0.0271-0.33040.14030.0150.0502-0.02010.2499-33.0462-31.988-19.0623
53.18180.9129-0.51293.0127-0.46113.11-0.24070.61210.2803-0.32220.26980.0407-0.0664-0.6214-0.0291-0.2175-0.19830.04130.1230.0505-0.2672-23.5219-51.5672-51.9606
61.53820.6144-0.88920.002-0.70890.7563-0.36950.2726-0.6041-0.1998-0.0046-0.02080.697-0.11690.3742-0.0233-0.16140.17590.0603-0.1196-0.2031-9.7591-74.9165-46.5099
70.22574.98033.885301.60664.4425-0.09010.1477-0.4568-0.5495-0.06780.34250.87120.01030.15790.3744-0.3040.12090.2219-0.304-0.4379-32.5436-81.6581-73.265
86.3688-4.8595-4.29315.4745.820800.05540.0717-0.35-0.48210.2008-0.1291-0.01580.247-0.25620.1036-0.3040.304-0.1512-0.3040.0042-28.4448-100.792-48.2847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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