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- PDB-5m5g: Crystal structure of the Chaetomium Thermophilum polycomb repress... -

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Basic information

Entry
Database: PDB / ID: 5m5g
TitleCrystal structure of the Chaetomium Thermophilum polycomb repressive complex 2 (PRC2)
Components
  • Fragment from molecular 2 (region containing putative polycomb protein Suz12)
  • HISTONE H3 11-Mer peptide
  • Putative uncharacterized protein
  • putative polycomb protein EED
KeywordsTRANSFERASE / REPRESSIVE / COMPLEX
Function / homology
Function and homology information


histone methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events ...histone methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / methylation / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus
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, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain ...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, VEFS-Box / VEFS-Box of polycomb protein / 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 / SET domain / SET domain profile. / 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 / Histone-fold / 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
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Zinc finger domain-containing protein / Uncharacterized protein / SET domain-containing protein / Histone H3.1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.27 Å
AuthorsZhang, Y. / Justin, N. / Wilson, J. / Gamblin, S.
Citation
Journal: Science / Year: 2016
Title: Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2".
Authors: Zhang, Y. / Justin, N. / Wilson, J.R. / Gamblin, S.J.
#1: Journal: Science / Year: 2015
Title: Structural Basis Of Histone H3K27 Trimethylation By An Active Polycomb Repressive Complex 2.
Authors: Jiao, L. / Liu, X.
History
DepositionOct 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative polycomb protein EED
B: Putative uncharacterized protein
D: HISTONE H3 11-Mer peptide
E: Fragment from molecular 2 (region containing putative polycomb protein Suz12)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,87113
Polymers174,9634
Non-polymers9089
Water9,512528
1
A: putative polycomb protein EED
D: HISTONE H3 11-Mer peptide


Theoretical massNumber of molelcules
Total (without water)67,1682
Polymers67,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area22240 Å2
MethodPISA
2
B: Putative uncharacterized protein
E: Fragment from molecular 2 (region containing putative polycomb protein Suz12)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,70311
Polymers107,7962
Non-polymers9089
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6 kcal/mol
Surface area45600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.554, 74.612, 128.508
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029920 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0S8H7
#2: Protein Putative uncharacterized protein


Mass: 106869.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SDW4

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Protein/peptide , 2 types, 2 molecules DE

#3: Protein/peptide HISTONE H3 11-Mer peptide


Mass: 1146.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#4: Protein/peptide Fragment from molecular 2 (region containing putative polycomb protein Suz12)


Mass: 926.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0RYC6*PLUS

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Non-polymers , 3 types, 537 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.46 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5CH1
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% PEG4000, 175mM ammonium citrate, pH 7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211.063
SYNCHROTRONAPS 19-ID20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 4, 2015
ADSC QUANTUM 3152CCDMar 4, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0631
20.9791
ReflectionResolution: 2.27→45.84 Å / Num. obs: 58693 / % possible obs: 90.69 % / Redundancy: 6.5 % / Net I/σ(I): 1.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.27→45.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.612 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22146 3147 5.1 %RANDOM
Rwork0.17088 ---
obs0.17343 58693 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å20.19 Å2
2--0.12 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.27→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10331 0 34 528 10893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01910648
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210001
X-RAY DIFFRACTIONr_angle_refined_deg1.721.95914416
X-RAY DIFFRACTIONr_angle_other_deg1.0373.00222997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57651273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6923.495515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.235151753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6561586
X-RAY DIFFRACTIONr_chiral_restr0.1020.21537
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111922
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022500
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3873.825159
X-RAY DIFFRACTIONr_mcbond_other3.3853.8195158
X-RAY DIFFRACTIONr_mcangle_it5.1575.6926407
X-RAY DIFFRACTIONr_mcangle_other5.1565.6926408
X-RAY DIFFRACTIONr_scbond_it4.0924.2985489
X-RAY DIFFRACTIONr_scbond_other4.0914.2995490
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5546.258010
X-RAY DIFFRACTIONr_long_range_B_refined8.98630.09611769
X-RAY DIFFRACTIONr_long_range_B_other8.98630.09811769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 124 -
Rwork0.231 2468 -
obs--51.83 %

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