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- PDB-6seg: Class1: CENP-A nucleosome in complex with CENP-C central region -

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Basic information

Entry
Database: PDB / ID: 6seg
TitleClass1: CENP-A nucleosome in complex with CENP-C central region
Components
  • (DNA (145-MER)) x 2
  • 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


condensed chromosome inner kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / nuclear pericentric heterochromatin / condensed nuclear chromosome kinetochore / condensed nuclear chromosome, centromeric region / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / establishment of mitotic spindle orientation / chromosome, centromeric region ...condensed chromosome inner kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / nuclear pericentric heterochromatin / condensed nuclear chromosome kinetochore / condensed nuclear chromosome, centromeric region / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / establishment of mitotic spindle orientation / chromosome, centromeric region / DNA replication-independent nucleosome assembly / telomere capping / chromatin silencing / mitotic cytokinesis / telomere organization / DNA replication-dependent nucleosome assembly / innate immune response in mucosa / nuclear nucleosome / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing by miRNA / nuclear chromosome / DNA-templated transcription, initiation / regulation of megakaryocyte differentiation / nucleosome assembly / nucleosome / double-strand break repair via nonhomologous end joining / chromatin organization / nuclear chromosome, telomeric region / antibacterial humoral response / antimicrobial humoral immune response mediated by antimicrobial peptide / protein ubiquitination / protein heterodimerization activity / defense response to Gram-positive bacterium / nuclear chromatin / protein domain specific binding / chromatin binding / cellular protein metabolic process / viral process / host cell nucleus / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol
Histone H4, conserved site / Histone H2A/H2B/H3 / Histone H3/CENP-A / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / Histone H2B / Histone H4 / Core histone H2A/H2B/H3/H4 / CENP-T/Histone H4, histone fold / Histone H2A conserved site ...Histone H4, conserved site / Histone H2A/H2B/H3 / Histone H3/CENP-A / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / Histone H2B / Histone H4 / Core histone H2A/H2B/H3/H4 / CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Histone H2A / TATA box binding protein associated factor (TAF) / Histone-fold / Histone, subunit A / Histone, subunit A / Orthogonal Bundle / Mainly Alpha
Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H2A type 2-A
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAli-Ahmad, A. / Bilokapic, S. / Schafer, I.B. / Halic, M. / Sekulic, N.
Funding support Norway, Germany, 2items
OrganizationGrant numberCountry
Research Council of Norway263195 Norway
European Research CouncilERC-smallRNAhet-309584 Germany
CitationJournal: EMBO Rep. / Year: 2019
Title: CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.
Authors: Ahmad Ali-Ahmad / Silvija Bilokapić / Ingmar B Schäfer / Mario Halić / Nikolina Sekulić /
Abstract: Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is ...Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C and CENP-C ) both bind exclusively to the CENP-A nucleosome. We find CENP-C to bind with high affinity due to an extended hydrophobic area made up of CENP-A and CENP-A . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C rigidifies the N-terminal tail of H4 in the conformation favoring H4 monomethylation, essential for a functional centromere.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 23, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name

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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)


Theoretical massNumber of molelcules
Total (without water)200,47410
Polymers200,47410
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53300 Å2
ΔGint-379 kcal/mol
Surface area71800 Å2
MethodPISA

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein 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 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, ...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 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 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 ...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

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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
IDNameTypeEntity IDParent-IDSource
1CENP-A nucleosomeCOMPLEX#1-#60MULTIPLE SOURCES
2Class1 : CENP-A nucleosome in complex with CENP-C central regionCOMPLEX#1-#41RECOMBINANT
3DNACOMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
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
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 320000 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006312496
ELECTRON MICROSCOPYf_angle_d0.84918125
ELECTRON MICROSCOPYf_chiral_restr0.05352059
ELECTRON MICROSCOPYf_plane_restr0.03651410
ELECTRON MICROSCOPYf_dihedral_angle_d25.85236452

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