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- PDB-9lrw: Cryo-EM structure of Fission yeast centromeric nucleosome Class 2 -

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Basic information

Entry
Database: PDB / ID: 9lrw
TitleCryo-EM structure of Fission yeast centromeric nucleosome Class 2
Components
  • (DNA (140-MER)) x 2
  • Histone H2A-alpha
  • Histone H2B-alpha
  • Histone H3-like centromeric protein cnp1
  • Histone H4
KeywordsNUCLEAR PROTEIN/DNA / Nucleosome dynamics / CENP-A / Cnp1 / kinetochore assembly / Chromosome Segregation / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


PKMTs methylate histone lysines / HDMs demethylate histones / CENP-A containing chromatin / : / Condensation of Prophase Chromosomes / HATs acetylate histones / : / : / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence ...PKMTs methylate histone lysines / HDMs demethylate histones / CENP-A containing chromatin / : / Condensation of Prophase Chromosomes / HATs acetylate histones / : / : / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / RMTs methylate histone arginines / Ub-specific processing proteases / HDACs deacetylate histones / chromosome, centromeric core domain / SUMOylation of chromatin organization proteins / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Transcriptional regulation by small RNAs / mating-type region heterochromatin / mitotic DNA damage checkpoint signaling / chromosome, subtelomeric region / CENP-A containing chromatin assembly / centromeric DNA binding / homologous chromosome segregation / rDNA heterochromatin / condensed chromosome, centromeric region / mitotic chromosome condensation / chromatin-protein adaptor activity / mitotic G2 DNA damage checkpoint signaling / chromosome, centromeric region / pericentric heterochromatin / CENP-A containing nucleosome / double-strand break repair via homologous recombination / structural constituent of chromatin / heterochromatin formation / nucleosome / double-strand break repair / nucleosome assembly / site of double-strand break / chromatin remodeling / protein heterodimerization activity / chromatin / DNA binding / nucleus
Similarity search - Function
: / 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 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 / 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) / Histone H2A-alpha / Histone H2B-alpha / Histone H4 / Histone H3-like centromeric protein cnp1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsXiong, Y. / Zang, J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J Mol Cell Biol / Year: 2025
Title: Cnp1 N-terminal dynamics regulate L1 loop recognition by Mis15 to orchestrate kinetochore assembly in Schizosaccharomyces pombe.
Authors: Yujie Xiong / Yanze Jian / Yongliang Zhang / Min Zhang / Xuan Zhang / Kaiming Zhang / Chuanhai Fu / Tian Tian / Jianye Zang /
Abstract: Centromeres are defined by the histone H3 variant CENP-A, which serve as the foundation for kinetochore assembly and ensure faithful chromosome segregation. CENP-A nucleosomes possess distinctive ...Centromeres are defined by the histone H3 variant CENP-A, which serve as the foundation for kinetochore assembly and ensure faithful chromosome segregation. CENP-A nucleosomes possess distinctive dynamic features, including flexible DNA ends at the entry/exit sites and a mobile N-terminal region, which are properties proposed to facilitate kinetochore assembly, yet the underlying molecular mechanisms remain elusive. Here, we present cryo-electron microscopy structures of Cnp1, the Schizosaccharomyces pombe (S. pombe) ortholog of CENP-A, alone and in complex with Mis15, the fission yeast ortholog of CENP-N. By integrating structural, biochemical, and molecular dynamics analyses, we demonstrate that the N-terminal region of Cnp1 regulates both DNA-end breathing and the conformational mobility of the L1 loop, a critical structural element for Mis15 recognition. Either enhanced dynamics caused by N-terminal deletion or reduced dynamics from targeted residue substitution disrupt Mis15 binding in vitro and impair its centromeric localization in vivo, thereby compromising the earliest steps of constitutive centromere-associated network assembly. Our findings establish the Cnp1 N-terminus as a dynamic allosteric modulator of chromatin architecture and reveal an L1 loop modulation mechanism that links nucleosome flexibility to kinetochore specification and chromosome segregation fidelity in fission yeast.
History
DepositionFeb 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3-like centromeric protein cnp1
B: Histone H4
C: Histone H2A-alpha
D: Histone H2B-alpha
E: Histone H3-like centromeric protein cnp1
F: Histone H4
G: Histone H2A-alpha
H: Histone H2B-alpha
I: DNA (140-MER)
J: DNA (140-MER)


Theoretical massNumber of molelcules
Total (without water)196,96010
Polymers196,96010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3-like centromeric protein cnp1 / Centromere protein 1 / CENP-A homolog / CENPA homolog / Silencing in the middle of the centromere protein 2


Mass: 13908.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: cnp1, sim2, SPBC1105.17
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: UniProt: Q9Y812
#2: Protein Histone H4


Mass: 11450.468 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: hhf1, h4.1, SPAC1834.03c, hhf2, h4.2, pi061, SPBC8D2.03c, hhf3, h4.3, SPBC1105.12
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: UniProt: P09322
#3: Protein Histone H2A-alpha / H2A.1


Mass: 13902.079 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: hta1, SPCC622.08c
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: UniProt: P04909
#4: Protein Histone H2B-alpha / H2B.1


Mass: 13844.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: htb1, SPCC622.09
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: UniProt: P04913

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (140-MER)


Mass: 45098.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
#6: DNA chain DNA (140-MER)


Mass: 45650.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)

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Details

Has protein modificationN

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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

ComponentName: Cryo-EM density maps of the Cnp1 nucleosome, with Class 2
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Source (recombinant)Organism: in vitro transcription vector pT7-Fluc(deltai) (others)
Buffer solutionpH: 7.5
SpecimenConc.: 0.2 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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1262686
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 832775 / Symmetry type: POINT
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411980
ELECTRON MICROSCOPYf_angle_d0.52617402
ELECTRON MICROSCOPYf_dihedral_angle_d32.2213584
ELECTRON MICROSCOPYf_chiral_restr0.0322001
ELECTRON MICROSCOPYf_plane_restr0.0041229

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