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- PDB-9wbj: cryo-EM structure of RIBEYE SAM thick filament -

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Basic information

Entry
Database: PDB / ID: 9wbj
Titlecryo-EM structure of RIBEYE SAM thick filament
ComponentsIsoform 2 of C-terminal-binding protein 2
KeywordsPROTEIN BINDING / RIBEYE / CTBP2 / ribbon synapse / filament
Function / homology
Function and homology information


Repression of WNT target genes / structural constituent of presynaptic active zone / positive regulation of retinoic acid receptor signaling pathway / Negative Regulation of CDH1 Gene Transcription / : / photoreceptor ribbon synapse / presynaptic active zone cytoplasmic component / ribbon synapse / nuclear retinoic acid receptor binding / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ...Repression of WNT target genes / structural constituent of presynaptic active zone / positive regulation of retinoic acid receptor signaling pathway / Negative Regulation of CDH1 Gene Transcription / : / photoreceptor ribbon synapse / presynaptic active zone cytoplasmic component / ribbon synapse / nuclear retinoic acid receptor binding / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / white fat cell differentiation / presynaptic cytosol / transcription repressor complex / transcription corepressor binding / transcription coregulator binding / cellular response to leukemia inhibitory factor / GABA-ergic synapse / NAD binding / transcription corepressor activity / DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol
Similarity search - Function
C-terminal binding protein / : / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
C-terminal-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsLiu, Y. / Niu, F. / Wei, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82188101 China
National Natural Science Foundation of China (NSFC)32471250 China
National Natural Science Foundation of China (NSFC)32400784 China
National Natural Science Foundation of China (NSFC)32471262 China
CitationJournal: Vita / Year: 2026
Title: Coordinated phase separation and phase transition underlie synaptic ribbon
Authors: 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.
History
DepositionAug 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 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: Isoform 2 of C-terminal-binding protein 2
B: Isoform 2 of C-terminal-binding protein 2
C: Isoform 2 of C-terminal-binding protein 2
D: Isoform 2 of C-terminal-binding protein 2
E: Isoform 2 of C-terminal-binding protein 2
F: Isoform 2 of C-terminal-binding protein 2
G: Isoform 2 of C-terminal-binding protein 2
H: Isoform 2 of C-terminal-binding protein 2
I: Isoform 2 of C-terminal-binding protein 2
J: Isoform 2 of C-terminal-binding protein 2
K: Isoform 2 of C-terminal-binding protein 2
L: Isoform 2 of C-terminal-binding protein 2
M: Isoform 2 of C-terminal-binding protein 2
N: Isoform 2 of C-terminal-binding protein 2
O: Isoform 2 of C-terminal-binding protein 2
P: Isoform 2 of C-terminal-binding protein 2
Q: Isoform 2 of C-terminal-binding protein 2
R: Isoform 2 of C-terminal-binding protein 2
S: Isoform 2 of C-terminal-binding protein 2
T: Isoform 2 of C-terminal-binding protein 2
U: Isoform 2 of C-terminal-binding protein 2
V: Isoform 2 of C-terminal-binding protein 2
W: Isoform 2 of C-terminal-binding protein 2
X: Isoform 2 of C-terminal-binding protein 2
Y: Isoform 2 of C-terminal-binding protein 2
Z: Isoform 2 of C-terminal-binding protein 2
a: Isoform 2 of C-terminal-binding protein 2
b: Isoform 2 of C-terminal-binding protein 2
c: Isoform 2 of C-terminal-binding protein 2
d: Isoform 2 of C-terminal-binding protein 2
e: Isoform 2 of C-terminal-binding protein 2
f: Isoform 2 of C-terminal-binding protein 2
g: Isoform 2 of C-terminal-binding protein 2
h: Isoform 2 of C-terminal-binding protein 2


Theoretical massNumber of molelcules
Total (without water)374,90234
Polymers374,90234
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Isoform 2 of C-terminal-binding protein 2 / RIBEYE / CtBP2


Mass: 11026.527 Da / Num. of mol.: 34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctbp2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56546
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: RIBEYE SAM domain / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 20 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv3.3.1particle selection
2SerialEM3.7image acquisition
4CTFFIND4CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCv3.3.1initial Euler assignment
10cryoSPARCv3.3.1final Euler assignment
11cryoSPARCv3.3.1classification
12cryoSPARCv3.3.13D reconstruction
13PHENIX1.18.2_3874model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -35.953 ° / Axial rise/subunit: 17 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 17495547
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 529850 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418020
ELECTRON MICROSCOPYf_angle_d0.68824378
ELECTRON MICROSCOPYf_dihedral_angle_d36.2482550
ELECTRON MICROSCOPYf_chiral_restr0.042890
ELECTRON MICROSCOPYf_plane_restr0.0043230

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