9OKL | pdb_00009okl

Structure of the Bombyx mori apo-bmCCAN

PDB DOI: https://doi.org/10.2210/pdb9OKL/pdb
EM Map EMD-70568: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Spodoptera frugiperda, Bombyx mori
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-05-10 Released: 2026-06-17
Deposition Author(s): Yatskevich, S., Ciferri, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Architecture and Function of Holocentric CENP-A-Independent Inner Kinetochores

Yatskevich, S., Ciferri, C.

To be published.

Macromolecule Content

Total Structure Weight: 483.84 kDa
Atom Count: 20,647
Modeled Residue Count: 2,569
Deposited Residue Count: 4,250
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CS-1	A	108	Spodoptera frugiperda	Mutation(s): 0
UniProt
Find proteins for A0A9R0D827 (Spodoptera frugiperda) Explore A0A9R0D827 Go to UniProtKB: A0A9R0D827
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0D827
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CS-2	B	82	Spodoptera frugiperda	Mutation(s): 0
UniProt
Find proteins for A0A2H1W2C4 (Spodoptera frugiperda) Explore A0A2H1W2C4 Go to UniProtKB: A0A2H1W2C4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2H1W2C4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SFRICE_007223	C	71	Spodoptera frugiperda	Mutation(s): 0
UniProt
Find proteins for A0A2H1VJ85 (Spodoptera frugiperda) Explore A0A2H1VJ85 Go to UniProtKB: A0A2H1VJ85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2H1VJ85
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CS-4	D	81	Spodoptera frugiperda	Mutation(s): 0

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
bm-CENPH	E [auth H]	239	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2AFF4 (Bombyx mori) Explore A0A8R2AFF4 Go to UniProtKB: A0A8R2AFF4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R2AFF4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein I	F [auth I]	661	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2LUB8 (Bombyx mori) Explore A0A8R2LUB8 Go to UniProtKB: A0A8R2LUB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R2LUB8
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-K	G [auth K]	219	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2AP23 (Bombyx mori) Explore A0A8R2AP23 Go to UniProtKB: A0A8R2AP23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R2AP23
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein L	H [auth L]	302	Bombyx mori	Mutation(s): 0 Gene Names: CYP340, 101745204
UniProt
Find proteins for H9IXB1 (Bombyx mori) Explore H9IXB1 Go to UniProtKB: H9IXB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H9IXB1
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein M	I [auth M]	180	Bombyx mori	Mutation(s): 0 Gene Names: 101745870
UniProt
Find proteins for A0A8R2ARQ0 (Bombyx mori) Explore A0A8R2ARQ0 Go to UniProtKB: A0A8R2ARQ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R2ARQ0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-N	J [auth N]	328	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R1WGT7 (Bombyx mori) Explore A0A8R1WGT7 Go to UniProtKB: A0A8R1WGT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R1WGT7
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein O	K [auth O]	325	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2AFZ4 (Bombyx mori) Explore A0A8R2AFZ4 Go to UniProtKB: A0A8R2AFZ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R2AFZ4
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-P	L [auth P]	638	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R1WGN9 (Bombyx mori) Explore A0A8R1WGN9 Go to UniProtKB: A0A8R1WGN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R1WGN9
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-T	M [auth T]	1,016	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2HRP3 (Bombyx mori) Explore A0A8R2HRP3 Go to UniProtKB: A0A8R2HRP3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R2HRP3
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Reference Sequence