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- PDB-9okd: Structure of the monomeric Bombyx mori CCAN bound to linear DNA -

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Basic information

Entry
Database: PDB / ID: 9okd
TitleStructure of the monomeric Bombyx mori CCAN bound to linear DNA
Components
  • (Centromere protein ...) x 4
  • (DNA (36-MER)) x 2
  • CS-1
  • CS-2
  • CS-4
  • DASH complex subunit DAD4
  • bmCENP-H
  • bmCENP-K
  • bmCENP-N
  • bmCENP-P
  • bmCENP-T
KeywordsDNA BINDING PROTEIN/DNA / CCAN / complex / protein-DNA / segregation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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
DNA / DNA (> 10) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Centromere protein O / Uncharacterized protein / Centromere protein M / Uncharacterized protein / Uncharacterized protein ...DNA / DNA (> 10) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Centromere protein O / Uncharacterized protein / Centromere protein M / Uncharacterized protein / Uncharacterized protein / Centromere protein I / Centromere protein L
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 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 9, 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: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half 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

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Assembly

Deposited unit
H: bmCENP-H
K: bmCENP-K
I: Centromere protein I
M: Centromere protein M
L: Centromere protein L
N: bmCENP-N
O: Centromere protein O
P: bmCENP-P
T: bmCENP-T
A: CS-1
C: DASH complex subunit DAD4
D: CS-4
B: CS-2
G: DNA (36-MER)
J: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)505,02215
Polymers505,02215
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 HKNPTACDB

#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: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R2AFF4
#2: 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: Trichoplusia ni (cabbage looper) / 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: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R1WGT7
#8: 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: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R1WGN9
#9: 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: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R2HRP3
#10: Protein CS-1


Mass: 10754.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Trichoplusia ni (cabbage looper)
#11: Protein DASH complex subunit DAD4


Mass: 8577.579 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R2AV77
#12: Protein CS-4


Mass: 9175.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Trichoplusia ni (cabbage looper)
#13: Protein CS-2


Mass: 9122.198 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Trichoplusia ni (cabbage looper)

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Centromere protein ... , 4 types, 4 molecules IMLO

#3: 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: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R2LUB8
#4: 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) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R2ARQ0
#5: 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) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H9IXB1
#7: 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: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8R2AFZ4

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DNA chain , 2 types, 2 molecules GJ

#14: DNA chain DNA (36-MER)


Mass: 11095.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (36-MER)


Mass: 11064.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (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: Bombyx mori CCAN monomer bound to DNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Bombyx mori (domestic silkworm)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
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
2EPUimage acquisition
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11RELIONclassification
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241975 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323634
ELECTRON MICROSCOPYf_angle_d0.43732246
ELECTRON MICROSCOPYf_dihedral_angle_d13.8829069
ELECTRON MICROSCOPYf_chiral_restr0.0453737
ELECTRON MICROSCOPYf_plane_restr0.0043836

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