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- PDB-6sef: Class2C : CENP-A nucleosome in complex with CENP-C central region -

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Basic information

Entry
Database: PDB / ID: 6sef
TitleClass2C : CENP-A nucleosome in complex with CENP-C central region
Components
  • (DNA (145-MER)) x 2
  • Centromere protein C
  • Histone H2A type 2-A
  • Histone H2B type 1-C/E/F/G/I
  • Histone H3-like centromeric protein A
  • Histone H4
KeywordsNUCLEAR PROTEIN / CENP-A / nucleosome / centromere / centromeric chromatin
Function / homology
Function and homology information


Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / Meiotic synapsis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Packaging Of Telomere Ends / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA ...Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / Meiotic synapsis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Packaging Of Telomere Ends / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / Senescence-Associated Secretory Phenotype (SASP) / Mitotic Prometaphase / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Deposition of new CENPA-containing nucleosomes at the centromere / G2/M DNA damage checkpoint / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Estrogen-dependent gene expression / Meiotic recombination / Amyloid fiber formation / RHO GTPases Activate Formins / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / DNA Damage/Telomere Stress Induced Senescence / Transcriptional regulation by small RNAs / DNA methylation / HDACs deacetylate histones / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / SUMOylation of chromatin organization proteins / NoRC negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / HDMs demethylate histones / HATs acetylate histones / attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation / condensed chromosome inner kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / nuclear pericentric heterochromatin / Flemming body / condensed nuclear chromosome kinetochore / negative regulation of megakaryocyte differentiation / condensed nuclear chromosome, centromeric region / CENP-A containing nucleosome assembly / establishment of mitotic spindle orientation / DNA replication-independent nucleosome assembly / cleavage furrow / telomere capping / chromosome, centromeric region / intercellular bridge / pericentric heterochromatin / mitotic cytokinesis / innate immune response in mucosa / telomere organization / DNA replication-dependent nucleosome assembly / nuclear nucleosome / chromatin silencing at rDNA / negative regulation of gene expression, epigenetic / nucleosomal DNA binding / kinetochore / regulation of gene silencing by miRNA / nuclear chromosome / DNA-templated transcription, initiation / chromosome segregation / regulation of megakaryocyte differentiation / nucleosome assembly / nucleosome / protein heterotetramerization / midbody / chromatin organization / mitotic cell cycle / double-strand break repair via nonhomologous end joining / nuclear body / antibacterial humoral response / nuclear chromosome, telomeric region / antimicrobial humoral immune response mediated by antimicrobial peptide / protein ubiquitination / defense response to Gram-positive bacterium / cell division / nuclear chromatin / protein domain specific binding / chromatin binding / viral process / cellular protein metabolic process
RmlC-like jelly roll fold / Histone H2B / Histone H3/CENP-A / Histone H2B signature. / Histone H3 signature 2. / Histone H2A / Histone H2A signature. / Histone H4 / TATA box binding protein associated factor (TAF) / Histone H2A, C-terminal domain ...RmlC-like jelly roll fold / Histone H2B / Histone H3/CENP-A / Histone H2B signature. / Histone H3 signature 2. / Histone H2A / Histone H2A signature. / Histone H4 / TATA box binding protein associated factor (TAF) / Histone H2A, C-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Centromere assembly component CENP-C middle DNMT3B-binding region / Centromere kinetochore component CENP-T histone fold / Mif2/CENP-C like / Core histone H2A/H2B/H3/H4 / CENP-T/Histone H4, histone fold / Histone H2A conserved site / CENP-C, middle DNMT3B-binding domain / Histone H2A/H2B/H3 / Centromere protein C/Mif2/cnp3 / Kinetochore assembly subunit CENP-C, N-terminal domain / Mif2/CENP-C cupin domain / Histone H4, conserved site / Histone H4 signature. / RmlC-like cupin domain superfamily / Histone-fold / C-terminus of histone H2A
Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Histone H2A type 2-A
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAli-Ahmad, A. / Bilokapic, S. / Schafer, I.B. / Halic, M. / Sekulic, N.
Funding support Norway, Germany, 2items
OrganizationGrant numberCountry
Norwegian Research Council263195 Norway
European Research CouncilERC-smallRNAhet-309584 Germany
CitationJournal: To Be Published
Title: CryoEM structure of human CENP-A nucleosome alone and in complex with central domain of human CENP-C
Authors: Ali-Ahmad, A. / Bilokapic, S. / Schafer, I.B. / Halic, M. / Sekulic, N.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Histone H3-like centromeric protein A
B: Histone H4
C: Histone H2A type 2-A
D: Histone H2B type 1-C/E/F/G/I
E: Histone H3-like centromeric protein A
F: Histone H4
G: Histone H2A type 2-A
H: Histone H2B type 1-C/E/F/G/I
I: DNA (145-MER)
J: DNA (145-MER)
V: Centromere protein C


Theoretical massNumber of molelcules
Total (without water)214,67811
Polymers214,67811
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54290 Å2
ΔGint-399 kcal/mol
Surface area75800 Å2
MethodPISA

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Components

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Protein/peptide , 5 types, 9 molecules AEBFCGDHV

#1: Protein/peptide Histone H3-like centromeric protein A / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 16023.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Production host: Escherichia coli (E. coli) / References: UniProt: P49450
#2: Protein/peptide Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein/peptide Histone H2A type 2-A / Histone H2A.2 / Histone H2A/o


Mass: 14125.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H2AA3, H2AFO, HIST2H2AA, HIST2H2AA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FI13
#4: Protein/peptide Histone H2B type 1-C/E/F/G/I / Histone H2B.1 A / Histone H2B.a / H2B/a / Histone H2B.g / H2B/g / Histone H2B.h / H2B/h / Histone H2B.k / H2B/k / Histone H2B.l / H2B/l


Mass: 13937.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
Production host: Escherichia coli (E. coli) / References: UniProt: P62807
#7: Protein/peptide Centromere protein C / / CENP-C / Centromere autoantigen C / Centromere protein C 1 / CENP-C 1 / Interphase centromere complex protein 7


Mass: 14204.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC, CENPC1, ICEN7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03188

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / 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

Type: COMPLEX

IDNameEntity IDParent-IDSource
1CENP-A nucleosome in complex with CENP-C central region1,2,3,4,5,6,70MULTIPLE SOURCES
2nucleosome1,2,3,4,71RECOMBINANT
3DNA5,61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33synthetic construct (others)32630
Source (recombinant)

Ncbi tax-ID: 562 / Organism: Escherichia coli (E. coli)

IDEntity assembly-ID
22
33
Buffer solutionpH: 7.5
SpecimenConc.: 1.2 mg/ml / Embedding 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 FIELDBright-field microscopy
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software

Classification: refinement / Version: 1.14_3260 / NB:

Name
phenix.real_space_refine
PHENIX
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40000 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.006912730
f_angle_d0.841818433
f_chiral_restr0.05172086
f_plane_restr0.00491322
f_dihedral_angle_d25.92466608

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