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- PDB-7td5: Structure of human PRC2-EZH1 containing phosphorylated SUZ12 -

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Basic information

Entry
Database: PDB / ID: 7td5
TitleStructure of human PRC2-EZH1 containing phosphorylated SUZ12
Components
  • (Polycomb protein ...Polycomb-group proteins) x 2
  • (THR-LYS-ALA-ALA-ARG- ...) x 2
  • Histone-lysine N-methyltransferase EZH1
KeywordsTRANSCRIPTION / Transcription regulatory complex / Histone modification
Function / homology
Function and homology information


[histone H3]-lysine27 N-trimethyltransferase / sex chromatin / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / facultative heterochromatin formation / histone H3K27 methyltransferase activity / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / lncRNA binding ...[histone H3]-lysine27 N-trimethyltransferase / sex chromatin / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / facultative heterochromatin formation / histone H3K27 methyltransferase activity / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / lncRNA binding / spinal cord development / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / negative regulation of cell differentiation / subtelomeric heterochromatin formation / anatomical structure morphogenesis / heterochromatin / nucleosome binding / enzyme activator activity / heterochromatin formation / methylated histone binding / SUMOylation of chromatin organization proteins / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / molecular condensate scaffold activity / promoter-specific chromatin binding / hippocampus development / chromatin DNA binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / chromosome / methylation / Oxidative Stress Induced Senescence / cell population proliferation / chromosome, telomeric region / nuclear body / chromatin remodeling / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
EZH1, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Ezh2, MCSS domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain ...EZH1, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Ezh2, MCSS domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain / CXC domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SET domain / SET domain profile. / SET domain / SANT/Myb domain / Zinc finger C2H2 type domain signature. / 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
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Polycomb protein EED / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsGong, L. / Jiao, L. / Liu, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2022
Title: CK2-mediated phosphorylation of SUZ12 promotes PRC2 function by stabilizing enzyme active site.
Authors: Gong, L. / Liu, X. / Jiao, L. / Yang, X. / Lemoff, A. / Liu, X.
History
DepositionDec 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EZH1
B: Polycomb protein EED
C: Polycomb protein SUZ12
D: THR-LYS-ALA-ALA-ARG-MET-SER-ALA-PRO-SER
E: THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA
F: Histone-lysine N-methyltransferase EZH1
G: Polycomb protein EED
H: Polycomb protein SUZ12
I: THR-LYS-ALA-ALA-ARG-MET-SER-ALA-PRO-SER
J: THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,78828
Polymers302,94410
Non-polymers1,84318
Water0
1
A: Histone-lysine N-methyltransferase EZH1
B: Polycomb protein EED
C: Polycomb protein SUZ12
D: THR-LYS-ALA-ALA-ARG-MET-SER-ALA-PRO-SER
E: THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,39414
Polymers151,4725
Non-polymers9229
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Histone-lysine N-methyltransferase EZH1
G: Polycomb protein EED
H: Polycomb protein SUZ12
I: THR-LYS-ALA-ALA-ARG-MET-SER-ALA-PRO-SER
J: THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,39414
Polymers151,4725
Non-polymers9229
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.870, 64.428, 254.496
Angle α, β, γ (deg.)90.00, 109.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AF

#1: Protein Histone-lysine N-methyltransferase EZH1 / ENX-2 / Enhancer of zeste homolog 1


Mass: 85394.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH1, KIAA0388 / Production host: Saccharomyces cerevisiae S288C (yeast)
References: UniProt: Q92800, [histone H3]-lysine27 N-trimethyltransferase

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Polycomb protein ... , 2 types, 4 molecules BGCH

#2: Protein Polycomb protein EED / / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 43170.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: O75530
#3: 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: 20841.514 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: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q15022

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THR-LYS-ALA-ALA-ARG- ... , 2 types, 4 molecules DIEJ

#4: Protein/peptide THR-LYS-ALA-ALA-ARG-MET-SER-ALA-PRO-SER


Mass: 1021.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Protein/peptide THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA


Mass: 1045.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 18 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 10% PEG3350, 100 mM (NH4)2SO4, 50mM HEPES 6.8

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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 6M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.994→50 Å / Num. obs: 72155 / % possible obs: 85.7 % / Redundancy: 6.6 % / CC1/2: 0.995 / Net I/σ(I): 19.15
Reflection shellResolution: 2.994→3.05 Å / Num. unique obs: 3560 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (16-JUL-2021)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WG6

5wg6


Resolution: 2.994→42.52 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.366
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 2988 -RANDOM
Rwork0.1957 ---
obs-61821 85.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.0739 Å20 Å25.6087 Å2
2--5.2862 Å20 Å2
3---6.7877 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.994→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16077 0 114 0 16191
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816543HARMONIC2
X-RAY DIFFRACTIONt_angle_deg122320HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5882SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2828HARMONIC5
X-RAY DIFFRACTIONt_it16543HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion21.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2103SEMIHARMONIC5
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_contact12292SEMIHARMONIC4
LS refinement shellResolution: 2.994→3.06 Å
RfactorNum. reflection% reflection
Rfree0.2542 -5.66 %
Rwork0.2535 1167 -
obs--27.8 %
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)
12.1959-0.0480.81820.3350.01970.956-0.07490.22820.3247-0.1596-0.0277-0.1494-0.27440.05250.1026-0.22680.11190.1217-0.14380.03520.104854.959897.977596.1182
24.02350.24721.46811.33180.50392.35620.2255-0.6597-0.3004-0.2469-0.2327-0.09880.2509-0.72790.0072-0.51740.19240.11850.1794-0.0177-0.019618.721689.502198.1939
33.4088-1.83630.23331.15190.75580.97630.0867-0.1623-0.27110.09310.046-0.0730.1287-0.1715-0.1328-0.19080.05440.082-0.0570.03670.275161.370586.2096104.998
4-0.10130.07770.19540.8804-0.21664.2057-0.0448-0.17850.0858-0.95070.09810.01350.71130.5387-0.05330.49790.24610.0166-0.3305-0.1069-0.492310.512481.682529.2824
50.78070.28320.64551.56180.1454.6311-0.042-0.30340.2273-0.8753-0.15740.5697-0.4471-0.50520.19940.18330.3298-0.3201-0.0578-0.11740.0036-5.891893.659556.4417
6-0.39540.5676-0.41810.8061-1.51265.33480.10180.18960.1838-0.58080.16290.0518-0.04330.3976-0.26460.68840.13180.0815-0.3072-0.0605-0.45778.4595.650515.8095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ F|* }
5X-RAY DIFFRACTION5{ G|* }
6X-RAY DIFFRACTION6{ H|* }

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