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- PDB-5wai: Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric ... -

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Basic information

Entry
Database: PDB / ID: 5wai
TitleCrystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex
Components
  • Histone-binding protein RBBP4
  • Jumonji, AT-rich interactive domain 2
  • Polycomb protein SUZ12
  • Zinc finger protein AEBP2
KeywordsTRANSCRIPTION / Methyltransferase
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / CAF-1 complex / random inactivation of X chromosome / negative regulation of cardiac muscle cell proliferation / histone H3K27 methyltransferase activity / sex chromatin / ubiquitin-modified histone reader activity / NURF complex / facultative heterochromatin formation / NuRD complex ...protein localization to pericentric heterochromatin / CAF-1 complex / random inactivation of X chromosome / negative regulation of cardiac muscle cell proliferation / histone H3K27 methyltransferase activity / sex chromatin / ubiquitin-modified histone reader activity / NURF complex / facultative heterochromatin formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / Polo-like kinase mediated events / RSC-type complex / Transcription of E2F targets under negative control by DREAM complex / chromatin silencing complex / histone H3K9me2/3 reader activity / ATPase complex / G1/S-Specific Transcription / lncRNA binding / histone deacetylase complex / Transcriptional Regulation by E2F6 / Sin3-type complex / positive regulation of stem cell population maintenance / histone methyltransferase complex / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / G0 and Early G1 / negative regulation of cell differentiation / cardiac muscle cell proliferation / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / spleen development / Regulation of TP53 Activity through Acetylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / thymus development / SUMOylation of chromatin organization proteins / ubiquitin binding / Regulation of PTEN gene transcription / central nervous system development / transcription corepressor binding / stem cell differentiation / cellular response to leukemia inhibitory factor / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / transcription coregulator activity / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / promoter-specific chromatin binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / negative regulation of transforming growth factor beta receptor signaling pathway / liver development / enzyme activator activity / protein-DNA complex / brain development / chromatin DNA binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / HCMV Early Events / nucleosome assembly / chromatin organization / regulation of gene expression / histone binding / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / cell population proliferation / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / ribonucleoprotein complex / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / Polycomb protein SUZ12-like, Zn domain / 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 / : / Zinc finger, C5HC2-type / C5HC2 zinc finger ...: / : / Polycomb protein SUZ12-like, Zn domain / 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 / : / Zinc finger, C5HC2-type / C5HC2 zinc finger / 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 / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger C2H2-type / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / 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. / 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 / Zinc finger protein AEBP2 / Protein Jumonji / Jumonji, AT-rich interactive domain 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Neovison vison (American mink)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
C: Zinc finger protein AEBP2
D: Jumonji, AT-rich interactive domain 2
E: Histone-binding protein RBBP4
F: Polycomb protein SUZ12
G: Zinc finger protein AEBP2
H: Jumonji, AT-rich interactive domain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,93910
Polymers237,8088
Non-polymers1312
Water00
1
A: Histone-binding protein RBBP4
B: Polycomb protein SUZ12
C: Zinc finger protein AEBP2
D: Jumonji, AT-rich interactive domain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9695
Polymers118,9044
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15690 Å2
ΔGint-40 kcal/mol
Surface area36170 Å2
MethodPISA
2
E: Histone-binding protein RBBP4
F: Polycomb protein SUZ12
G: Zinc finger protein AEBP2
H: Jumonji, AT-rich interactive domain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9695
Polymers118,9044
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-38 kcal/mol
Surface area34660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.300, 111.428, 253.254
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.: 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 / 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: Protein Zinc finger protein AEBP2 / Adipocyte enhancer-binding protein 2 / AE-binding protein 2


Mass: 11592.598 Da / Num. of mol.: 2 / Fragment: UNP residues 191-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AEBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZN18
#4: Protein/peptide Jumonji, AT-rich interactive domain 2


Mass: 2257.717 Da / Num. of mol.: 2 / Fragment: UNP residues 39-57 / Source method: obtained synthetically / Source: (synth.) Neovison vison (American mink) / References: UniProt: U6DXQ8, UniProt: Q92833*PLUS
#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: 2.83 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG6000, 5%v/v(+/-)-2-Methyl-2,4-pentaneediol (MPD) and 100mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→48.1 Å / Num. obs: 67533 / % possible obs: 99.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 68.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.042 / Net I/σ(I): 22.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 12.6 % / Rmerge(I) obs: 2.851 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2989 / CC1/2: 0.472 / Rpim(I) all: 0.828 / % possible all: 99.8

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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: 2.9→48.1 Å / Cor.coef. Fo:Fc: 0.9356 / Cor.coef. Fo:Fc free: 0.8975 / SU R Cruickshank DPI: 0.777 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.685 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 2867 5.02 %RANDOM
Rwork0.1711 ---
obs0.1734 57060 94.14 %-
Displacement parametersBiso mean: 66.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.4092 Å20 Å20 Å2
2---3.8092 Å20 Å2
3---5.2184 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.9→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12899 0 2 0 12901
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113211HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.217875HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4627SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes337HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1864HARMONIC5
X-RAY DIFFRACTIONt_it13211HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion21.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1700SEMIHARMONIC5
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_contact14054SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2437 122 4.58 %
Rwork0.231 2541 -
all0.2316 2663 -
obs--60.23 %
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)
12.514-0.379-0.50711.63620.00432.4532-0.27710.0123-0.37590.1330.13020.27910.245-0.29070.147-0.2591-0.00210.0906-0.11730.0708-0.06281.29649.18031.8843
21.2768-0.3007-0.35060.578-0.14911.19070.03330.5658-0.0064-0.2596-0.05850.0170.0343-0.14970.0251-0.2590.0257-0.04510.01820.0259-0.235713.219714.5303-23.5116
32.2552-1.06540.71061.73690.02552.37810.03531.0885-0.0669-0.4620.14120.34430.0017-0.2581-0.1765-0.2152-0.091-0.07670.31480.0533-0.278811.474313.7092-33.5017
44.4201-4.60824.46080.4053.22176.14680.00120.0275-0.2807-0.2458-0.04180.0840.0130.24790.0407-0.04040.01070.14920.12280.0704-0.107739.514316.5347-26.2502
52.2703-1.4185-0.62373.76970.44482.86370.26510.19090.28970.066-0.1157-0.0832-0.3492-0.6122-0.1494-0.06980.11530.0791-0.30020.0685-0.1995-9.836-16.48448.3078
60.9595-0.9282-0.39062.13030.11240.91370.27160.2240.0959-0.1652-0.2188-0.58740.1050.0386-0.0528-0.13810.04180.0721-0.32320.0383-0.14517.7949-37.198835.7463
73.22290.1977-0.64262.8623-0.34183.30940.01670.2081-0.1494-0.5297-0.2736-1.08360.49930.19070.2568-0.06360.27680.1792-0.25710.20630.010614.3004-37.5129.4719
84.15415.5001-3.03972.79981.01022.658-0.06390.353-0.10090.07790.12120.05690.16340.2087-0.05730.1569-0.0065-0.0002-0.1745-0.19620.00342.7452-62.671440.3104
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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