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- PDB-9okk: Bombyx mori bmCENP-LN-HIKM sub-complex structure -

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Basic information

Entry
Database: PDB / ID: 9okk
TitleBombyx mori bmCENP-LN-HIKM sub-complex structure
Components
  • (Centromere protein ...) x 3
  • bmCENP-H
  • bmCENP-K
  • bmCENP-N
  • bmCENP-T
KeywordsCELL CYCLE / DNA-protein / segregation / CCAN / kinetochore
Function / homology
Function and homology information


CENP-A containing chromatin assembly / inner kinetochore / mitotic sister chromatid segregation / chromosome, centromeric region / nucleus
Similarity search - Function
Centromere subunit L / Centromere protein L / Centromere protein Cenp-M / Centromere protein M (CENP-M) / Centromere protein I / Mis6 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Centromere protein M / Uncharacterized protein / Centromere protein I / Centromere protein L
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsYatskevich, S. / Ciferri, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2026
Title: Architecture and function of holocentric CENP-A-independent inner kinetochores.
Authors: Christine Yu / Sundar Ram Sankaranarayanan / Gaetan Cornilleau / Anna C Howes / Caleigh M Azumaya / Eric S Day / Inna Zilberleyb / Bobby Brillantes / Tommy K Cheung / Leonie Dec / Damarys ...Authors: Christine Yu / Sundar Ram Sankaranarayanan / Gaetan Cornilleau / Anna C Howes / Caleigh M Azumaya / Eric S Day / Inna Zilberleyb / Bobby Brillantes / Tommy K Cheung / Leonie Dec / Damarys Loew / Phong Tran / Christopher M Rose / Ines Anna Drinnenberg / Claudio Ciferri / Stanislau Yatskevich /
Abstract: Kinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of ...Kinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of kinetochores across diverse species remains poorly understood. We present the inner kinetochore constitutive centromere-associated network (CCAN) structure of the silkmoth , an insect that lacks the canonical centromere-specifying histone variant CENP-A and exhibits chromosome-wide centromeric activity (holocentric). The CCAN incorporates four previously uncharacterized centromeric subunit proteins that are structurally related to the Dam1/DASH complex but function in scaffolding the inner kinetochore rather than in microtubule binding. Similar to the yeast and human systems, the CCAN also entraps DNA within its central closed chamber. However, unlike these systems, the CCAN can also assemble in vitro into a self-contained head-to-head dimer via atypical histone-fold protein dimerization. On the basis of our findings, we propose that the holocentric organization may emerge from the modular arrangement of discrete kinetochore units.
History
DepositionMay 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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

Downloads & links

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Assembly

Deposited unit
H: bmCENP-H
I: Centromere protein I
K: bmCENP-K
L: Centromere protein L
M: Centromere protein M
N: bmCENP-N
T: bmCENP-T


Theoretical massNumber of molelcules
Total (without water)336,4517
Polymers336,4517
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules HKNT

#1: Protein bmCENP-H


Mass: 27719.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8R2AFF4
#3: Protein bmCENP-K


Mass: 24760.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8R2AP23
#6: Protein bmCENP-N


Mass: 36883.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8R1WGT7
#7: Protein bmCENP-T


Mass: 116758.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8R2HRP3

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Centromere protein ... , 3 types, 3 molecules ILM

#2: Protein Centromere protein I / bmCENP-I


Mass: 75965.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8R2LUB8
#4: Protein Centromere protein L / bmCENP-L


Mass: 34229.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: CYP340, 101745204 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: H9IXB1
#5: Protein Centromere protein M / bmCENP-M


Mass: 20135.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: 101745870 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8R2ARQ0

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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: Bombyx mori bmCENP-LN-HIKM sub-complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bombyx mori (domestic silkworm)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.20.1_4487:model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237375 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039498
ELECTRON MICROSCOPYf_angle_d0.48412850
ELECTRON MICROSCOPYf_dihedral_angle_d3.871249
ELECTRON MICROSCOPYf_chiral_restr0.0731521
ELECTRON MICROSCOPYf_plane_restr0.0031615

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