+Open data
-Basic information
Entry | Database: PDB / ID: 7on1 | |||||||||
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Title | Cenp-A nucleosome in complex with Cenp-C | |||||||||
Components |
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Keywords | CELL CYCLE / Kinetochore / Nucleosome / Complex | |||||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Yan, K. / Yang, J. / Zhang, Z. / Barford, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Cenp-A nucleosome in complex with Cenp-C Authors: Yan, K. / Yang, J. / Zhang, Z. / Barford, D. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7on1.cif.gz | 295.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7on1.ent.gz | 205.6 KB | Display | PDB format |
PDBx/mmJSON format | 7on1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7on1_validation.pdf.gz | 776.2 KB | Display | wwPDB validaton report |
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Full document | 7on1_full_validation.pdf.gz | 782.5 KB | Display | |
Data in XML | 7on1_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 7on1_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/7on1 ftp://data.pdbj.org/pub/pdb/validation_reports/on/7on1 | HTTPS FTP |
-Related structure data
Related structure data | 12993MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 10 molecules CDbfdheagc
#1: Protein | Mass: 62553.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS3513, PACBIOSEQ_LOCUS3568, PACBIOSEQ_LOCUS3643, PACBIOSEQ_LOCUS3923, SCNYR20_0010011700, SCP684_0010011600 Cell line (production host): Hi 5 / Production host: unidentified baculovirus / References: UniProt: A0A6A5PSM0 #2: Protein | Mass: 11523.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS211, PACBIOSEQ_LOCUS221, PACBIOSEQ_LOCUS224, PACBIOSEQ_LOCUS227, PACBIOSEQ_LOCUS231, PACBIOSEQ_LOCUS238, PACBIOSEQ_LOCUS256, PACBIOSEQ_LOCUS257, PACBIOSEQ_LOCUS4758, PACBIOSEQ_ ...Gene: PACBIOSEQ_LOCUS211, PACBIOSEQ_LOCUS221, PACBIOSEQ_LOCUS224, PACBIOSEQ_LOCUS227, PACBIOSEQ_LOCUS231, PACBIOSEQ_LOCUS238, PACBIOSEQ_LOCUS256, PACBIOSEQ_LOCUS257, PACBIOSEQ_LOCUS4758, PACBIOSEQ_LOCUS5031, PACBIOSEQ_LOCUS5100, PACBIOSEQ_LOCUS5103, PACBIOSEQ_LOCUS5119, PACBIOSEQ_LOCUS5144, PACBIOSEQ_LOCUS5156, PACBIOSEQ_LOCUS5208, PACBIOSEQ_LOCUS5512, PACBIOSEQ_LOCUS5605, SCNYR20_0007010300, SCNYR20_0008026600, SCP684_0007010000, SCP684_0008026100 Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q1V3 #3: Protein | Mass: 14408.493 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS1150, PACBIOSEQ_LOCUS1153, PACBIOSEQ_LOCUS1155, PACBIOSEQ_LOCUS1161, PACBIOSEQ_LOCUS1171, PACBIOSEQ_LOCUS1174, PACBIOSEQ_LOCUS1245, PACBIOSEQ_LOCUS1286, SCNYR20_0001041200, SCP684_0001040800 Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PZQ7 #4: Protein | Mass: 27013.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS3556, PACBIOSEQ_LOCUS3600, PACBIOSEQ_LOCUS3611, PACBIOSEQ_LOCUS3648, SCP684_0010015800 Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PV75 #5: Protein | Mass: 14141.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS1081, PACBIOSEQ_LOCUS1151, PACBIOSEQ_LOCUS1154, PACBIOSEQ_LOCUS1156, PACBIOSEQ_LOCUS1162, PACBIOSEQ_LOCUS1172, PACBIOSEQ_LOCUS1175, PACBIOSEQ_LOCUS1287, SCNYR20_0001041300, SCP684_0001040900 Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q1K4 |
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-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 45138.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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#7: DNA chain | Mass: 38125.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 39 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124953 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.62 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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