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- PDB-9okl: Structure of the Bombyx mori apo-bmCCAN -

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Basic information

Entry
Database: PDB / ID: 9okl
TitleStructure of the Bombyx mori apo-bmCCAN
Components
  • (Centromere protein ...) x 4
  • CS-1
  • CS-2
  • CS-4
  • SFRICE_007223
  • bm-CENPH
  • bmCENP-K
  • bmCENP-N
  • bmCENP-P
  • bmCENP-T
KeywordsDNA BINDING PROTEIN / CCAN / complex / protein-DNA / segregation
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
SFRICE_007223 / SFRICE_005847 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Centromere protein O / Uncharacterized protein / Centromere protein M / Uncharacterized protein / Centromere protein I ...SFRICE_007223 / SFRICE_005847 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Centromere protein O / Uncharacterized protein / Centromere protein M / Uncharacterized protein / Centromere protein I / Uncharacterized protein LOC118271842 / Centromere protein L
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
Spodoptera frugiperda (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsYatskevich, S. / Ciferri, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Architecture and Function of Holocentric CENP-A-Independent Inner Kinetochores
Authors: Yatskevich, S. / Ciferri, C.
History
DepositionMay 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 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
A: CS-1
B: CS-2
C: SFRICE_007223
D: CS-4
H: bm-CENPH
I: Centromere protein I
K: bmCENP-K
L: Centromere protein L
M: Centromere protein M
N: bmCENP-N
O: Centromere protein O
P: bmCENP-P
T: bmCENP-T


Theoretical massNumber of molelcules
Total (without water)483,84113
Polymers483,84113
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 , 9 types, 9 molecules ABCDHKNPT

#1: Protein CS-1


Mass: 12255.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A9R0D827
#2: Protein CS-2


Mass: 9024.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2H1W2C4
#3: Protein SFRICE_007223


Mass: 8090.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2H1VJ85
#4: Protein CS-4


Mass: 9237.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm)
#5: Protein bm-CENPH


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
#7: 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
#10: 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
#12: Protein bmCENP-P


Mass: 71100.820 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: A0A8R1WGN9
#13: 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 ... , 4 types, 4 molecules ILMO

#6: 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
#8: 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
#9: 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
#11: Protein Centromere protein O / bmCENP-O


Mass: 37681.129 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: A0A8R2AFZ4

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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 CCAN dimer bound to DNA / 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
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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
3EPUimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265941 / Symmetry type: POINT

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