9OKB | pdb_00009okb

Structure of the dimeric Bombyx mori CCAN bound to DNA

PDB DOI: https://doi.org/10.2210/pdb9OKB/pdb
EM Map EMD-70558: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Bombyx mori, synthetic construct
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-05-09 Released: 2026-06-17
Deposition Author(s): Yatskevich, S., Ciferri, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 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: 1,001.54 kDa
Atom Count: 45,518
Modeled Residue Count: 5,484
Deposited Residue Count: 8,592
Unique protein chains: 13
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CS-1	A, Q [auth a]	95	Bombyx mori	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CS-2	B, R [auth b]	82	Bombyx mori	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CS-3	C, S [auth c]	72	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2AV77 (Bombyx mori) Explore A0A8R2AV77 Go to UniProtKB: A0A8R2AV77
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8R2AV77
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CS-4	D, T [auth d]	81	Bombyx mori	Mutation(s): 0

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-H	E [auth H], U [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], V [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
Centromere protein M	G [auth J], J [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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-K	H [auth K], W [auth k]	219	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2AP23 (Bombyx mori) Explore A0A8R2AP23 Go to UniProtKB: A0A8R2AP23
Entity Groups
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UniProt Group	A0A8R2AP23
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein L	I [auth L], X [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: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-N	K [auth N], Y [auth n]	328	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R1WGT7 (Bombyx mori) Explore A0A8R1WGT7 Go to UniProtKB: A0A8R1WGT7
Entity Groups
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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	L [auth O], Z [auth o]	325	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R2AFZ4 (Bombyx mori) Explore A0A8R2AFZ4 Go to UniProtKB: A0A8R2AFZ4
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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	AA [auth p], M [auth P]	638	Bombyx mori	Mutation(s): 0
UniProt
Find proteins for A0A8R1WGN9 (Bombyx mori) Explore A0A8R1WGN9 Go to UniProtKB: A0A8R1WGN9
Entity Groups
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UniProt Group	A0A8R1WGN9
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
bmCENP-T	BA [auth t], N [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

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Molecule	Chains	Length	Organism
Entity ID: 14
DNA (58-MER)	O [auth X]	58	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA (58-MER)	P [auth Y]	58	synthetic construct
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CA [auth T] MOL2 format, chain CA [auth T] mmCIF format, chain CA [auth T]	CA [auth T]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth T] Interactions & Density Focus chain CA [auth T]