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- PDB-7on1: Cenp-A nucleosome in complex with Cenp-C -

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Basic information

Entry
Database: PDB / ID: 7on1
TitleCenp-A nucleosome in complex with Cenp-C
Components
  • BJ4_G0006610.mRNA.1.CDS.1
  • BJ4_G0007000.mRNA.1.CDS.1
  • DNA (123-MER)
  • DNA (152-MER)
  • Histone H2A
  • Histone H2B
  • Histone H4
KeywordsCELL 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
Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like jelly roll fold / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B ...Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like jelly roll fold / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / MIF2 isoform 1 / CSE4 isoform 1 / Histone H2B / Histone H2A / Histone H4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsYan, K. / Yang, J. / Zhang, Z. / Barford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: To Be Published
Title: Cenp-A nucleosome in complex with Cenp-C
Authors: Yan, K. / Yang, J. / Zhang, Z. / Barford, D.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
C: BJ4_G0006610.mRNA.1.CDS.1
b: Histone H4
d: Histone H2B
e: BJ4_G0007000.mRNA.1.CDS.1
f: Histone H4
g: Histone H2A
h: Histone H2B
c: Histone H2A
I: DNA (152-MER)
J: DNA (123-MER)
a: BJ4_G0007000.mRNA.1.CDS.1
D: BJ4_G0006610.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)342,54512
Polymers342,54512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area50390 Å2
ΔGint-349 kcal/mol
Surface area72860 Å2
MethodPISA

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Components

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Protein , 5 types, 10 molecules CDbfdheagc

#1: Protein BJ4_G0006610.mRNA.1.CDS.1 / BJ4_G0032560.mRNA.1.CDS.1 / HLJ1_G0003950.mRNA.1.CDS.1 / Inner kinetochore subunit MIF2 / Y55_ ...BJ4_G0032560.mRNA.1.CDS.1 / HLJ1_G0003950.mRNA.1.CDS.1 / Inner kinetochore subunit MIF2 / Y55_G0004160.mRNA.1.CDS.1


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 Histone H4


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 Histone H2B


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 BJ4_G0007000.mRNA.1.CDS.1 / HLJ1_G0004330.mRNA.1.CDS.1 / HN1_G0004320.mRNA.1.CDS.1 / Histone H3-like centromeric protein CSE4 / ...HLJ1_G0004330.mRNA.1.CDS.1 / HN1_G0004320.mRNA.1.CDS.1 / Histone H3-like centromeric protein CSE4 / SX2_G0004350.mRNA.1.CDS.1


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 Histone H2A


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 DNA (152-MER)


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)
#7: DNA chain DNA (123-MER)


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)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cenp-A nucleosome in complex with Cenp-CCOMPLEXall0MULTIPLE SOURCES
2Kinetochore subunitCOMPLEX#11RECOMBINANT
3HistonesCOMPLEX#2-#51RECOMBINANT
4DNA (152-MER), DNA (123-MER)COMPLEX#6-#71RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (brewer's yeast)4932
23Saccharomyces cerevisiae (brewer's yeast)4932
34Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12unidentified baculovirus10469
23Escherichia coli (E. coli)562
34Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.16_3549refinement
PHENIX1.16_3549refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124953 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 84.62 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002411843
ELECTRON MICROSCOPYf_angle_d0.42317056
ELECTRON MICROSCOPYf_chiral_restr0.0291955
ELECTRON MICROSCOPYf_plane_restr0.00281299
ELECTRON MICROSCOPYf_dihedral_angle_d21.54076275

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