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- PDB-5kji: Crystal structure of an active polycomb repressive complex 2 in t... -

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Basic information

Entry
Database: PDB / ID: 5kji
TitleCrystal structure of an active polycomb repressive complex 2 in the basal state
Components
  • Putative uncharacterized protein,Zinc finger domain-containing protein
  • putative polycomb protein Eed
KeywordsTRANSFERASE / Complex / Methyltransferase
Function / homology
Function and homology information


[histone H3]-lysine27 N-trimethyltransferase / histone H3K27 methyltransferase activity / heterochromatin formation / chromatin organization / methylation / chromatin binding / zinc ion binding / 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 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 superfamily / SET domain profile. / SET domain / 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-ADENOSYL-L-HOMOCYSTEINE / Polycomb protein SUZ12 / Polycomb protein EED / Histone-lysine N-methyltransferase EZH2
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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 20, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionApr 19, 2017ID: 5CH2
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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,Zinc finger domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,79911
Polymers172,8912
Non-polymers9089
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-44 kcal/mol
Surface area54140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.333, 74.619, 127.035
Angle α, β, γ (deg.)90.00, 105.63, 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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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,Zinc finger domain-containing 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), (gene. exp.) Chaetomium thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230, CTHT_0006210 / Production host: Saccharomyces cerevisiae S288c (yeast) / References: UniProt: G0SDW4, UniProt: G0RYC6
#3: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
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: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 40497 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 58.6 Å2 / Rsym value: 0.046 / Net I/σ(I): 26.18
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1.72 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KJH

5kjh


Resolution: 2.71→47.31 Å / Cor.coef. Fo:Fc: 0.9255 / Cor.coef. Fo:Fc free: 0.8687 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.35
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1826 4.93 %RANDOM
Rwork0.1793 ---
obs0.1827 37042 91.22 %-
Displacement parametersBiso mean: 48.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.7148 Å20 Å2-2.8232 Å2
2--8.3478 Å20 Å2
3----6.633 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: 1 / Resolution: 2.71→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9883 0 34 111 10028
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110152HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1313746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3499SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes252HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1474HARMONIC5
X-RAY DIFFRACTIONt_it10152HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion19.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1284SEMIHARMONIC5
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_contact11146SEMIHARMONIC4
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.37 46 3.55 %
Rwork0.2102 1251 -
all0.2161 1297 -
obs--41.45 %
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)
11.1529-0.3783-0.15071.24060.81211.9256-0.1174-0.32310.01030.20360.2053-0.06270.27260.331-0.0879-0.12270.03010.0006-0.03340.0389-0.2159109.30370.8133275.2979
21.0057-0.58870.00940.83380.11580.9034-0.1054-0.13390.02810.13620.03030.1097-0.0245-0.18570.0751-0.2263-0.07290.0008-0.0394-0.0316-0.250976.231993.6085273.5429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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