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- PDB-6chg: Crystal structure of the yeast COMPASS catalytic module -

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Basic information

Entry
Database: PDB / ID: 6chg
TitleCrystal structure of the yeast COMPASS catalytic module
Components
  • H3
  • Histone-lysine N-methyltransferase, H3 lysine-4 specific
  • KLLA0A08800p
  • KLLA0C10945p
  • KLLA0E03521p
  • KLLA0E24487p
KeywordsTRANSFERASE / Histones / S-adenosylmethionine / Complex / enzyme
Function / homology
Function and homology information


[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / chromosome / histone binding / methylation / transcription cis-regulatory region binding / RNA binding / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N ...Histone-lysine N-methyltransferase Set1, fungi / Histone lysine methyltransferase SET associated / : / Histone lysine methyltransferase SET associated / Histone-lysine N-methyltransferase, RNA-binding domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / COMPASS complex Set1 subunit, N-SET domain / Histone-lysine N-methyltransferase Set1-like / COMPASS (Complex proteins associated with Set1p) component N / COMPASS (Complex proteins associated with Set1p) component N / : / Dpy-30 motif / Dpy-30 motif / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Beta Complex / WD domain, G-beta repeat / Concanavalin A-like lectin/glucanase domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 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
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-4 specific / KLLA0E24487p / KLLA0E03521p / KLLA0C10945p / KLLA0A08800p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.985 Å
AuthorsHsu, P.L. / Li, H. / Zheng, N.
CitationJournal: Cell / Year: 2018
Title: Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module.
Authors: Hsu, P.L. / Li, H. / Lau, H.T. / Leonen, C. / Dhall, A. / Ong, S.E. / Chatterjee, C. / Zheng, N.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: KLLA0E24487p
B: KLLA0C10945p
C: Histone-lysine N-methyltransferase, H3 lysine-4 specific
D: KLLA0A08800p
E: KLLA0E03521p
F: KLLA0E03521p
J: H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,1979
Polymers163,7337
Non-polymers4642
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.839, 138.319, 136.133
Angle α, β, γ (deg.)90.00, 112.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 5 types, 6 molecules ABCDEF

#1: Protein KLLA0E24487p


Mass: 34793.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E24487g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CLY5
#2: Protein KLLA0C10945p


Mass: 47286.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_C10945g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CTQ1
#3: Protein Histone-lysine N-methyltransferase, H3 lysine-4 specific / COMPASS component SET1 / SET domain-containing protein 1


Mass: 17420.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: SET1, KLLA0F24134g / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6CIT4, histone-lysine N-methyltransferase
#4: Protein KLLA0A08800p


Mass: 49894.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_A08800g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CXF3
#5: Protein KLLA0E03521p


Mass: 6900.937 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E03521g / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6CPN6

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Protein/peptide , 1 types, 1 molecules J

#6: Protein/peptide H3


Mass: 535.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 12 molecules

#7: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.34 Å3/Da / Density % sol: 71.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium Tartrate, PEG20000, ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.985→50 Å / Num. obs: 54818 / % possible obs: 96.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Rrim(I) all: 0.165 / Net I/σ(I): 14.73
Reflection shellResolution: 2.985→3.05 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.175 / Num. unique obs: 2416 / CC1/2: 0.569 / Rpim(I) all: 0.474 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F6K, 2H14

5f6k

2h14


Resolution: 2.985→44.607 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 2771 5.09 %
Rwork0.228 --
obs0.2301 54476 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.985→44.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10599 0 28 10 10637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310854
X-RAY DIFFRACTIONf_angle_d0.61314696
X-RAY DIFFRACTIONf_dihedral_angle_d15.4686503
X-RAY DIFFRACTIONf_chiral_restr0.0471633
X-RAY DIFFRACTIONf_plane_restr0.0041865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9853-3.03670.3891060.3211790X-RAY DIFFRACTION68
3.0367-3.09190.35241120.31562331X-RAY DIFFRACTION87
3.0919-3.15140.40721340.31112441X-RAY DIFFRACTION89
3.1514-3.21570.35431140.30252483X-RAY DIFFRACTION93
3.2157-3.28560.341330.2982543X-RAY DIFFRACTION94
3.2856-3.3620.31671460.27842534X-RAY DIFFRACTION94
3.362-3.4460.33291440.26962582X-RAY DIFFRACTION95
3.446-3.53920.29671230.27392589X-RAY DIFFRACTION96
3.5392-3.64330.31831630.26912628X-RAY DIFFRACTION98
3.6433-3.76080.31121450.25932684X-RAY DIFFRACTION99
3.7608-3.89520.28441430.25062668X-RAY DIFFRACTION100
3.8952-4.0510.31121370.24222702X-RAY DIFFRACTION100
4.051-4.23520.25141540.21712695X-RAY DIFFRACTION100
4.2352-4.45830.24481380.19762750X-RAY DIFFRACTION100
4.4583-4.73740.21121400.1792673X-RAY DIFFRACTION100
4.7374-5.10270.22451510.18922722X-RAY DIFFRACTION100
5.1027-5.61530.29941430.20142696X-RAY DIFFRACTION100
5.6153-6.42580.27281550.23432709X-RAY DIFFRACTION100
6.4258-8.08790.24761440.22622740X-RAY DIFFRACTION100
8.0879-44.61150.21271460.19222745X-RAY DIFFRACTION99

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