+Open data
-Basic information
Entry | Database: PDB / ID: 6chg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the yeast COMPASS catalytic module | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / Histones / S-adenosylmethionine / Complex / enzyme | ||||||
Function / homology | Function and homology information [histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / chromosome / methylation Similarity search - Function | ||||||
Biological species | Kluyveromyces lactis (yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.985 Å | ||||||
Authors | Hsu, P.L. / Li, H. / Zheng, N. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6chg.cif.gz | 507.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6chg.ent.gz | 416 KB | Display | PDB format |
PDBx/mmJSON format | 6chg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6chg ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6chg | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 5 types, 6 molecules ABCDEF
#1: Protein | 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 | 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 | 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 | 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 | 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 |
-Protein/peptide , 1 types, 1 molecules J
#6: Protein/peptide | Mass: 535.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
---|
-Non-polymers , 3 types, 12 molecules
#7: Chemical | ChemComp-SAM / |
---|---|
#8: Chemical | ChemComp-ZN / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.68 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Sodium Tartrate, PEG20000, ATP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.985→44.607 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|