[English] 日本語
Yorodumi
- EMDB-54544: Gephyrin E-Domain dimer of dimers - local refinement of dimer A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54544
TitleGephyrin E-Domain dimer of dimers - local refinement of dimer A
Map data
Sample
  • Complex: Gephyrin E-domain homotetramer in Gephyrin full length context
    • Other: Gephyrin
Keywordsscaffolding protein / postsynaptic density / protein-protein interaction / linker-mediated regulation / STRUCTURAL PROTEIN
Function / homologymolybdopterin adenylyltransferase / molybdopterin molybdotransferase / Isoform 5 of Gephyrin
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsOrtiz-Lopez D / Hove T / Boettcher B / Schindelin H
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)232550447 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)525040890 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of higher order Gephyrin oligomers reveal principles of inhibitory postsynaptic scaffold organization.
Authors: Diego Ortiz-López / Tamsanqa T Hove / Christiane Huhn / Serena Camuso / Pia M van Gen Hassend / Bodo Sander / Benjamin F N Campbell / Shiva K Tyagarajan / Andreas Plückthun / Christian G ...Authors: Diego Ortiz-López / Tamsanqa T Hove / Christiane Huhn / Serena Camuso / Pia M van Gen Hassend / Bodo Sander / Benjamin F N Campbell / Shiva K Tyagarajan / Andreas Plückthun / Christian G Specht / Hans M Maric / Bettina Böttcher / Hermann Schindelin /
Abstract: Gephyrin, the principal scaffolding protein of inhibitory postsynaptic densities, clusters glycine and GABA receptors via multivalent interactions. It features structured N and C terminal domains ...Gephyrin, the principal scaffolding protein of inhibitory postsynaptic densities, clusters glycine and GABA receptors via multivalent interactions. It features structured N and C terminal domains connected by an intrinsically disordered linker. Although the structural and functional properties of its terminal domains are well characterized, the mechanism by which full-length gephyrin organizes into higher-order complexes remains unresolved. Here, we combine biochemical reconstitution, cryo-electron microscopy, and mutational analyses to elucidate the structural logic of gephyrin oligomerization. We demonstrate that gephyrin adopts a stable dimeric assembly which constitutes the basic unit for both linear and oblique tetramers as well as linear hexameric arrangements. High resolution structures reveal a critical segment of the flexible linker that adopts two distinct conformations, one of which occludes the receptor-binding site. This segment harbors key phosphorylation sites, suggesting a regulatory control mechanism. Our findings redefine the architecture of inhibitory postsynaptic sites and reconcile gephyrin oligomerization models with published in-situ postsynaptic densities characterized by cryo-electron tomography.
History
DepositionJul 24, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54544.png

Downloads & links

-
Map

FileDownload / File: emd_54544.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 240 pix.
= 337.92 Å		1.41 Å/pix.
x 240 pix.
= 337.92 Å		1.41 Å/pix.
x 240 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.408 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00518
Minimum - Maximum-0.018707369 - 0.04374115
Average (Standard dev.)-0.00012490958 (±0.0006614466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_54544_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54544_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Gephyrin E-domain homotetramer in Gephyrin full length context

EntireName: Gephyrin E-domain homotetramer in Gephyrin full length context
Components
  • Complex: Gephyrin E-domain homotetramer in Gephyrin full length context
    • Other: Gephyrin

-
Supramolecule #1: Gephyrin E-domain homotetramer in Gephyrin full length context

SupramoleculeName: Gephyrin E-domain homotetramer in Gephyrin full length context
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 350 KDa

-
Macromolecule #1: Gephyrin

MacromoleculeName: Gephyrin / type: other / ID: 1 / Classification: other
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString: MAHHHHHHGG SSGGSSEFMA TEGMILTNHD HQIRVGVLTV SDSCFRNLAE DRSGINLKDL VQDPSLLGGT ISAYKIVPDE IEEIKETLID WCDEKELNLI LTTGGTGFAP RDVTPEATKE VIEREAPGMA LAMLMGSLNV TPLGMLSRPV CGIRGKTLII NLPGSKKGSQ ...String:
MAHHHHHHGG SSGGSSEFMA TEGMILTNHD HQIRVGVLTV SDSCFRNLAE DRSGINLKDL VQDPSLLGGT ISAYKIVPDE IEEIKETLID WCDEKELNLI LTTGGTGFAP RDVTPEATKE VIEREAPGMA LAMLMGSLNV TPLGMLSRPV CGIRGKTLII NLPGSKKGSQ ECFQFILPAL PHAIDLLRDA IVKVKEVHDE LEDLPSPPPP LSPPPTTSPH KQTEDKGVQC EEEEEEKKDS GVASTEDSSS SHITAAALAA KIPDSIISRG VQVLPRDTAS LSTTPSESPR AQATSRLSTA SCPTPKVQSR CSSKENILRA SHSAVDITKV ARRHRMSPFP LTSMDKAFIT VLEMTPVLGT EIINYRDGMG RVLAQDVYAK DNLPPFPASV KDGYAVRAAD GPGDRFIIGE SQAGEQPTQT VMPGQVMRVT TGAPIPCGAD AVVQVEDTEL IRESDDGTEE LEVRILVQAR PGQDIRPIGH DIKRGECVLA KGTHMGPSEI GLLATVGVTE VEVNKFPVVA VMSTGNELLN PEDDLLPGKI RDSNRSTLLA TIQEHGYPTI NLGIVGDNPD DLLNALNEGI SRADVIITSG GVSMGEKDYL KQVLDIDLHA QIHFGRVFMK PGLPTTFATL DIDGVRKIIF ALPGNPVSAV VTCNLFVVPA LRKMQGILDP RPTIIKARLS CDVKLDPRPE YHRCILTWHH QEPLPWAQST GNQMSSRLMS MRSANGLLML PPKTEQYVEL HKGEVVDVMV IGRL

UniProtKB: Isoform 5 of Gephyrin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloride
5.0 mMC2H6OS2-mercaptoethanol
1.0 mMC10H16N2O8EDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.1 sec. / Average electron dose: 42.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction using CryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Details: Local refinement of one dimer from consensus map. / Number images used: 283182
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final 3D classificationSoftware - Name: RELION (ver. 5)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more