9LRV | pdb_00009lrv

Cryo-EM structure of Fission yeast centromeric nucleosome Class 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Cnp1 N-terminal dynamics regulate L1 loop recognition by Mis15 to orchestrate kinetochore assembly in Schizosaccharomyces pombe.

Xiong, Y.Jian, Y.Zhang, Y.Zhang, M.Zhang, X.Zhang, K.Fu, C.Tian, T.Zang, J.

(2025) J Mol Cell Biol 

  • DOI: https://doi.org/10.1093/jmcb/mjaf056
  • Primary Citation Related Structures: 
    9LRV, 9LRW

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Health Management Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China.

Macromolecule Content 

  • Total Structure Weight: 197.79 kDa 
  • Atom Count: 11,645 
  • Modeled Residue Count: 1,030 
  • Deposited Residue Count: 1,262 
  • Unique protein chains: 5
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein cnp1126Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cnp1sim2SPBC1105.17
UniProt
Find proteins for Q9Y812 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9Y812 
Go to UniProtKB:  Q9Y812
Entity Groups
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UniProt GroupQ9Y812
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: hhf1h4.1SPAC1834.03chhf2h4.2pi061SPBC8D2.03chhf3h4.3SPBC1105.12
UniProt
Find proteins for P09322 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P09322 
Go to UniProtKB:  P09322
Entity Groups
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UniProt GroupP09322
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A-alpha
C, G
132Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: hta1SPCC622.08c
UniProt
Find proteins for P04909 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P04909 
Go to UniProtKB:  P04909
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UniProt GroupP04909
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B-alpha
D, H
126Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: htb1SPCC622.09
UniProt
Find proteins for P04913 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P04913 
Go to UniProtKB:  P04913
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UniProt GroupP04913
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein cnp1120Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cnp1sim2SPBC1105.17
UniProt
Find proteins for Q9Y812 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9Y812 
Go to UniProtKB:  Q9Y812
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y812
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (144-MER)147Schizosaccharomyces pombe 972h-
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (144-MER)147Schizosaccharomyces pombe 972h-
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release