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- EMDB-65843: cryo-EM structure of RIBEYE B' filament -

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Basic information

Entry
Database: EMDB / ID: EMD-65843
Titlecryo-EM structure of RIBEYE B' filament
Map data
Sample
  • Complex: RIBEYE B' domain
    • Protein or peptide: Isoform 2 of C-terminal-binding protein 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
KeywordsRIBEYE / CTBP2 / ribbon synapse / filament / PROTEIN BINDING
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsLiu Y / Niu F / Wei Z
Funding support China, 4 items
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, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65843.png

Downloads & links

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Map

FileDownload / File: emd_65843.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 384 pix.
= 353.28 Å		0.92 Å/pix.
x 384 pix.
= 353.28 Å		0.92 Å/pix.
x 384 pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.001789876 - 2.1897626
Average (Standard dev.)0.0040882826 (±0.047045626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65843_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65843_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RIBEYE B' domain

EntireName: RIBEYE B' domain
Components
  • Complex: RIBEYE B' domain
    • Protein or peptide: Isoform 2 of C-terminal-binding protein 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: RIBEYE B' domain

SupramoleculeName: RIBEYE B' domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Isoform 2 of C-terminal-binding protein 2

MacromoleculeName: Isoform 2 of C-terminal-binding protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 49.028668 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HMGSARRTGA PIIVSTMLTP EPSIRPQIMN GPLHPRPLVA LLDGRDCTVE MPILKDLATV AFCDAQSTQE IHEKVLNEAV GAMMYHTIT LTREDLEKFK ALRVIVRIGS GYDNVDIKAA GELGIAVCNI PSAAVEETAD STVCHILNLY RRNTWLYQAL R EGTRVQSV ...String:
HMGSARRTGA PIIVSTMLTP EPSIRPQIMN GPLHPRPLVA LLDGRDCTVE MPILKDLATV AFCDAQSTQE IHEKVLNEAV GAMMYHTIT LTREDLEKFK ALRVIVRIGS GYDNVDIKAA GELGIAVCNI PSAAVEETAD STVCHILNLY RRNTWLYQAL R EGTRVQSV EQIREVASGA ARIRGETLGL IGFGRTGQAV AVRAKAFGFS VIFYDPYLQD GIERSLGVQR VYTLQDLLYQ SD CVSLHCN LNEHNHHLIN DFTIKQMRQG AFLVNAARGG LVDEKALAQA LKEGRIRGAA LDVHESEPFS FAQGPLKDAP NLI CTPHTA WYSEQASLEM REAAATEIRR AITGRIPESL RNCVNKEFFV TSAPWSVIDQ QAIHPELNGA TYRYPPGIVG VAPG GLPPA MEGIIPGGIP VTHNLPTVAH PSQAPSPNQP TKHGDNREHP NEQ

UniProtKB: C-terminal-binding protein 2

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 20 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Details: 20 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM EDTA, 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 55.737 Å
Applied symmetry - Helical parameters - Δ&Phi: -157.078 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.1) / Number images used: 113042
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: NONE
Segment selectionNumber selected: 7756421 / Software - Name: cryoSPARC (ver. v3.3.1)
Startup modelType of model: OTHER / Details: ab initio intial model
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. v3.3.1)

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Atomic model buiding 1

Initial modelPDB ID:

6wkw


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9wbl:
cryo-EM structure of RIBEYE B' filament

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