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- EMDB-54821: Gephyrin E domain dimer D422N variant -

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Basic information

Entry
Database: EMDB / ID: EMD-54821
TitleGephyrin E domain dimer D422N variant
Map data
Sample
  • Complex: Gephyrin E domain dimer
    • Protein or peptide: Gephyrin E domain D422N
KeywordsDimer / filament / scaffolding / inhibitory synapse / PROTEIN BINDING
Function / homology
Function and homology information


Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase activity / molybdopterin adenylyltransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / molybdopterin molybdotransferase / gamma-aminobutyric acid receptor clustering ...Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase activity / molybdopterin adenylyltransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / molybdopterin molybdotransferase / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / molybdopterin cofactor binding / postsynaptic specialization, intracellular component / response to metal ion / neurotransmitter receptor localization to postsynaptic specialization membrane / synaptic transmission, GABAergic / protein targeting / synapse assembly / synaptic membrane / establishment of protein localization / tubulin binding / GABA-ergic synapse / cytoplasmic side of plasma membrane / molecular adaptor activity / dendritic spine / cytoskeleton / protein-macromolecule adaptor activity / postsynaptic membrane / postsynaptic density / postsynapse / signaling receptor binding / neuronal cell body / dendrite / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Molybdenum cofactor biosynthesis proteins signature 2. / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdenum cofactor biosynthesis, conserved site ...Molybdenum cofactor biosynthesis proteins signature 2. / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMacha A / Gunkel M / Schwarz G / Behrmann E / Burdina N
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
CitationJournal: Nat Commun / Year: 2025
Title: Gephyrin filaments represent the molecular basis of inhibitory postsynaptic densities.
Authors: Arthur Macha / Filip Liebsch / Emanuel H W Bruckisch / Nele Burdina / Imke von Stülpnagel / Konrad Benting / Monika Gunkel / Elmar Behrmann / Guenter Schwarz /
Abstract: The multifunctional protein gephyrin clusters inhibitory receptors at the postsynaptic membrane in the CNS. Gephyrin has been proposed to form the inhibitory postsynaptic density by liquid-liquid ...The multifunctional protein gephyrin clusters inhibitory receptors at the postsynaptic membrane in the CNS. Gephyrin has been proposed to form the inhibitory postsynaptic density by liquid-liquid phase separation, involving a complex interplay between receptor binding and oligomerization via its conserved G- and E-domains. Here we show by single particle cryo-EM analysis that dimerization promotes the formation of gephyrin filaments in which two E-domain dimers are linked by Z-shaped interfaces formed between two subdomains II (SDII) of adjacent dimers. Deletion of SDII, introduction of two epilepsy-causing pathogenic variants, or neutralization of an opposing charge in the interface abolish the formation of filaments, in vitro phase separation, and synaptic receptor clustering in hippocampal neurons. In conclusion, this work identifies gephyrin E-domain filaments as the structural foundation underlying gephyrin both phase separation and receptor clustering at inhibitory postsynaptic densities.
History
DepositionAug 19, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54821.png

Downloads & links

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Map

FileDownload / File: emd_54821.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.84 Å		0.86 Å/pix.
x 320 pix.
= 275.84 Å		0.86 Å/pix.
x 320 pix.
= 275.84 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-5.2313643 - 6.6198664
Average (Standard dev.)0.00026361833 (±0.12229015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54821_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: #1

Fileemd_54821_additional_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: DeepEMhanced map

Fileemd_54821_additional_2.map
AnnotationDeepEMhanced map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_54821_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54821_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Gephyrin E domain dimer

EntireName: Gephyrin E domain dimer
Components
  • Complex: Gephyrin E domain dimer
    • Protein or peptide: Gephyrin E domain D422N

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Supramolecule #1: Gephyrin E domain dimer

SupramoleculeName: Gephyrin E domain dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 93 KDa

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Macromolecule #1: Gephyrin E domain D422N

MacromoleculeName: Gephyrin E domain D422N / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO / EC number: molybdopterin adenylyltransferase
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRGSHHHHHH GSACELGTDK AFITVLEMTP VLGTEIINYR DGMGRVLAQD VYAKDNLPPF PASVKDGYAV RAADGPGDRF IIGESQAGE QPTQTVMPGQ VMRVTTGAPI PCGANAVVQV EDTELIRESD DGTEELEVRI LVQARPGQDI RPIGHDIKRG E CVLAKGTH ...String:
MRGSHHHHHH GSACELGTDK AFITVLEMTP VLGTEIINYR DGMGRVLAQD VYAKDNLPPF PASVKDGYAV RAADGPGDRF IIGESQAGE QPTQTVMPGQ VMRVTTGAPI PCGANAVVQV EDTELIRESD DGTEELEVRI LVQARPGQDI RPIGHDIKRG E CVLAKGTH MGPSEIGLLA TVGVTEVEVN KFPVVAVMST GNELLNPEDD LLPGKIRDSN RSTLLATIQE HGYPTINLGI VG DNPDDLL NALNEGISRA DVIITSGGVS MGEKDYLKQV LDIDLHAQIH FGRVFMKPGL PTTFATLDID GVRKIIFALP GNP VSAVVT CNLFVVPALR KMQGILDPRP TIIKARLSCD VKLDPRPEYH RCILTWHHQE PLPWAQSTGN QMSSRLMSMR SANG LLMLP PKTEQYVELH KGEVVDVMVI GRL

UniProtKB: Gephyrin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
250.0 mMNaClSodium chloride
5.0 mMC2H6OSMercaptoethanol
25.0 mMC5H8NNaO4Monosodiumglutamate
25.0 mMH2NC(NH)NH(CH2)3CH(NH2)CO2HArginin
1.0 %C12H22O11Sucrose
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailsmonodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2609 / Average exposure time: 43.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1646000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Software - details: patchCTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio reconstruction
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: non-uniform refinement / Number images used: 78000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Software - details: ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Software - details: non-uniform refinement
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4) / Software - details: 3D classification
FSC plot (resolution estimation)

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