9WBL | pdb_00009wbl

cryo-EM structure of RIBEYE B' filament

PDB DOI: https://doi.org/10.2210/pdb9WBL/pdb
EM Map EMD-65843: EMDB EMDataResource

Classification: PROTEIN BINDING
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-14 Released: 2026-06-03
Deposition Author(s): Liu, Y., Niu, F., Wei, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.41 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Coordinated phase separation and phase transition underlie synaptic ribbon

Liu, Y., Wang, X., Zheng, T., Niu, F., Sun, R., Yang, C., Xu, S., Zhao, Z., Shen, Z., Huang, W., Wang, X., Liu, K., Cai, S., Zhang, M., Wei, Z.

(2026) Vita

DOI: https://doi.org/10.15302/vita.2026.05.0033

Macromolecule Content

Total Structure Weight: 993.84 kDa
Atom Count: 54,720
Modeled Residue Count: 6,936
Deposited Residue Count: 8,960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of C-terminal-binding protein 2	A B C D [auth E] E [auth F] A, B, C, D [auth E], E [auth F], F [auth H], G [auth D], H [auth G], I, J, K, L, M, N, O, P, Q, R, S, T	448	Mus musculus	Mutation(s): 0 Gene Names: Ctbp2
UniProt & NIH Common Fund Data Resources
Find proteins for P56546 (Mus musculus) Go to UniProtKB: P56546
IMPC: MGI:1201686
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56546-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain DA [auth J] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain GA [auth M] SDF format, chain HA [auth N] SDF format, chain IA [auth O] SDF format, chain JA [auth P] SDF format, chain KA [auth Q] SDF format, chain LA [auth R] SDF format, chain MA [auth S] SDF format, chain NA [auth T] SDF format, chain U [auth A] SDF format, chain W [auth C] SDF format, chain X [auth E] SDF format, chain Y [auth F] SDF format, chain Z [auth H] SDF format, chain V [auth B] SDF format, chain CA [auth I] SDF format, chain BA [auth G] SDF format, chain AA [auth D] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain HA [auth N] MOL2 format, chain IA [auth O] MOL2 format, chain JA [auth P] MOL2 format, chain KA [auth Q] MOL2 format, chain LA [auth R] MOL2 format, chain MA [auth S] MOL2 format, chain NA [auth T] MOL2 format, chain U [auth A] MOL2 format, chain W [auth C] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth H] MOL2 format, chain V [auth B] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth D] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain HA [auth N] mmCIF format, chain IA [auth O] mmCIF format, chain JA [auth P] mmCIF format, chain KA [auth Q] mmCIF format, chain LA [auth R] mmCIF format, chain MA [auth S] mmCIF format, chain NA [auth T] mmCIF format, chain U [auth A] mmCIF format, chain W [auth C] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth H] mmCIF format, chain V [auth B] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth G] CA [auth I] DA [auth J] EA [auth K] AA [auth D], BA [auth G], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth N], IA [auth O], JA [auth P], KA [auth Q], LA [auth R], MA [auth S], NA [auth T], U [auth A], V [auth B], W [auth C], X [auth E], Y [auth F], Z [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth Q] Focus chain LA [auth R] Focus chain MA [auth S] Focus chain NA [auth T] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.41 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v3.3.1
MODEL REFINEMENT	PHENIX	1.18.2_3874

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Liu, Y.

Niu, F.

Wei, Z.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82188101
National Natural Science Foundation of China (NSFC)	China	32471250
National Natural Science Foundation of China (NSFC)	China	32400784
National Natural Science Foundation of China (NSFC)	China	32471262