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- PDB-5kkl: Structure of ctPRC2 in complex with H3K27me3 and H3K27M -

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Basic information

Entry
Database: PDB / ID: 5kkl
TitleStructure of ctPRC2 in complex with H3K27me3 and H3K27M
Components
  • ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA
  • Putative uncharacterized protein,Histone H3.1 peptide,Zinc finger domain-containing protein
  • putative polycomb protein Eed
KeywordsTRANSFERASE / Complex / Methyltransferase / Histone H3
Function / homology
Function and homology information


[histone H3]-lysine27 N-trimethyltransferase / histone H3K27 methyltransferase activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation ...[histone H3]-lysine27 N-trimethyltransferase / histone H3K27 methyltransferase activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / methylation / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / metal ion binding / nucleus / membrane
Similarity search - Function
EZH2, N-terminal domain / MCSS domain / : / : / Fungal MCSS domain / EZH2 N-terminal domain / Fungal polycomb repressive complex 2, Ezh2-like, preSET CXC domain / Polycomb protein EED insertion domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein ...EZH2, N-terminal domain / MCSS domain / : / : / Fungal MCSS domain / EZH2 N-terminal domain / Fungal polycomb repressive complex 2, Ezh2-like, preSET CXC domain / Polycomb protein EED insertion domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / WD domain, G-beta repeat / 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
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Polycomb protein SUZ12 / Polycomb protein EED / Histone-lysine N-methyltransferase EZH2 / Histone H3.1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsJiao, L. / Liu, X.
CitationJournal: Science / Year: 2016
Title: Response to Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2".
Authors: Jiao, L. / Liu, X.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative polycomb protein Eed
B: Putative uncharacterized protein,Histone H3.1 peptide,Zinc finger domain-containing protein
D: ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,98012
Polymers174,0583
Non-polymers9229
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-53 kcal/mol
Surface area57930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.254, 80.559, 133.220
Angle α, β, γ (deg.)90.00, 107.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative polycomb protein Eed


Mass: 66021.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029920 / Production host: Saccharomyces cerevisiae S288c (yeast) / References: UniProt: G0S8H7
#2: Protein Putative uncharacterized protein,Histone H3.1 peptide,Zinc finger domain-containing protein


Mass: 106890.555 Da / Num. of mol.: 1 / Mutation: K2027M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Homo sapiens (human)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230 / Production host: Saccharomyces cerevisiae S288c (yeast)
References: UniProt: G0SDW4, UniProt: P68431, UniProt: G0RYC6
#3: Protein/peptide ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA


Mass: 1146.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG4000, 175mM ammonium citrate, pH 7.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 36440 / % possible obs: 98 % / Redundancy: 6.5 % / Biso Wilson estimate: 65.81 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 24.15
Reflection shellResolution: 2.94→3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1739 / % possible all: 94.7

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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: 5KJH

5kjh


Resolution: 2.94→48.74 Å / Cor.coef. Fo:Fc: 0.8784 / Cor.coef. Fo:Fc free: 0.8319 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1517 4.89 %RANDOM
Rwork0.1862 ---
obs0.1885 31019 82.98 %-
Displacement parametersBiso mean: 78.88 Å2
Baniso -1Baniso -2Baniso -3
1-14.552 Å20 Å222.4542 Å2
2---13.0106 Å20 Å2
3----1.5415 Å2
Refine analyzeLuzzati coordinate error obs: 0.351 Å
Refinement stepCycle: 1 / Resolution: 2.94→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10567 0 35 0 10602
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910874HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0514741HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3753SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes276HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1579HARMONIC5
X-RAY DIFFRACTIONt_it10874HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion21.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1378SEMIHARMONIC5
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_contact11701SEMIHARMONIC4
LS refinement shellResolution: 2.94→3.04 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2879 45 4.4 %
Rwork0.2312 977 -
all0.2335 1022 -
obs--29.87 %
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)
11.9053-0.4961-0.63871.47951.51572.9393-0.197-0.7507-0.07490.3030.3625-0.07460.56890.9053-0.16550.1790.18310.375-0.04240.1112-0.1738105.6355.2447284.6228
22.7736-0.3318-0.70150.66730.27432.09330.1414-0.37960.44520.0617-0.08720.2593-0.2291-0.3431-0.05420.07930.01570.4033-0.5276-0.05-0.06572.102577.1196285.0397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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