[English] 日本語
Yorodumi
- EMDB-52402: The one:one complex of gephyrin and collybistin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52402
TitleThe one:one complex of gephyrin and collybistin
Map dataGeph-CB-1:1 complex, combined particles from Folch and non-Folch datasets
Sample
  • Complex: The one:one complex of gephyrin and collybistin
    • Complex: Gephyrin dimer
      • Protein or peptide: Gephyrin
    • Complex: two copies of collybistin 2 (-SH3)
      • Protein or peptide: Collybistin 2 (-SH3)
KeywordsPSD / postsynaptic density / scaffolding protein / inhibitory synapse / LIPID BINDING PROTEIN
Function / homologymolybdopterin adenylyltransferase / molybdopterin molybdotransferase / Isoform 5 of Gephyrin / Isoform 2 of Rho guanine nucleotide exchange factor 9
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBurdina N / Behrmann E / Schwarz G
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
German Research Foundation (DFG)RTG2550/1 project ID 411422114 Germany
CitationJournal: To Be Published
Title: Structural basis of gephyrin filament formation regulated by collybistin and lipids
Authors: Burdina N / Liebsch F / Macha A / Behrmann E / Schwarz G
History
DepositionDec 21, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52402.png

Downloads & links

-
Map

FileDownload / File: emd_52402.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGeph-CB-1:1 complex, combined particles from Folch and non-Folch datasets
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 300 pix.
= 441.3 Å		1.47 Å/pix.
x 300 pix.
= 441.3 Å		1.47 Å/pix.
x 300 pix.
= 441.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.471 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.25
Minimum - Maximum-7.0489364 - 10.692695000000001
Average (Standard dev.)-0.00051935023 (±0.11811518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 441.3 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Geph-CB-1:1 complex, particles from Folch dataset

Fileemd_52402_additional_1.map
AnnotationGeph-CB-1:1 complex, particles from Folch dataset
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Geph-CB-1:1 complex, combined particles from Folch and non-Folch...

Fileemd_52402_additional_2.map
AnnotationGeph-CB-1:1 complex, combined particles from Folch and non-Folch datasets - deepEMhancer, sharpened version
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Geph-CB-1:1 complex, particles from non-Folch dataset

Fileemd_52402_additional_3.map
AnnotationGeph-CB-1:1 complex, particles from non-Folch dataset
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Geph-CB-1:1 complex, combined particles from Folch and non-Folch...

Fileemd_52402_half_map_1.map
AnnotationGeph-CB-1:1 complex, combined particles from Folch and non-Folch datasets - even particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Geph-CB-1:1 complex, combined particles from Folch and non-Folch...

Fileemd_52402_half_map_2.map
AnnotationGeph-CB-1:1 complex, combined particles from Folch and non-Folch datasets - odd particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The one:one complex of gephyrin and collybistin

EntireName: The one:one complex of gephyrin and collybistin
Components
  • Complex: The one:one complex of gephyrin and collybistin
    • Complex: Gephyrin dimer
      • Protein or peptide: Gephyrin
    • Complex: two copies of collybistin 2 (-SH3)
      • Protein or peptide: Collybistin 2 (-SH3)

-
Supramolecule #1: The one:one complex of gephyrin and collybistin

SupramoleculeName: The one:one complex of gephyrin and collybistin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 102 KDa

-
Supramolecule #2: Gephyrin dimer

SupramoleculeName: Gephyrin dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Supramolecule #3: two copies of collybistin 2 (-SH3)

SupramoleculeName: two copies of collybistin 2 (-SH3) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Macromolecule #1: Gephyrin

MacromoleculeName: Gephyrin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: molybdopterin adenylyltransferase
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGSHHHHHH GSACELGTMA TEGMILTNHD HQIRVGVLTV SDSCFRNLAE DRSGINLKDL VQDPSLLGGT ISAYKIVPDE IEEIKETLID WCDEKELNLI LTTGGTGFAP RDVTPEATKE VIEREAPGMA LAMLMGSLNV TPLGMLSRPV CGIRGKTLII NLPGSKKGSQ ...String:
MRGSHHHHHH GSACELGTMA 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

-
Macromolecule #2: Collybistin 2 (-SH3)

MacromoleculeName: Collybistin 2 (-SH3) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGSHHHHHH GSACELGTMQ WIRGGSGMLW VNQEDGVEEG PSDVQNGHLD PNSDCLCLGR PLQNRDQMRA NVINEIMSTE RHYIKHLKDI CEGYLKQCRK RRDMFSDEQL KVIFGNIEDI YRFQMGFVRD LEKQYNNDDP HLSEIGPCFL EHQDGFWIYS EYCNNHLDAC ...String:
MRGSHHHHHH GSACELGTMQ WIRGGSGMLW VNQEDGVEEG PSDVQNGHLD PNSDCLCLGR PLQNRDQMRA NVINEIMSTE RHYIKHLKDI CEGYLKQCRK RRDMFSDEQL KVIFGNIEDI YRFQMGFVRD LEKQYNNDDP HLSEIGPCFL EHQDGFWIYS EYCNNHLDAC MELSKLMKDS RYQHFFEACR LLQQMIDIAI DGFLLTPVQK ICKYPLQLAE LLKYTAQDHS DYRYVAAALA VMRNVTQQIN ERKRRLENID KIAQWQASVL DWEGDDILDR SSELIYTGEM AWIYQPYGRN QQRVFFLFDH QMVLCKKDLI RRDILYYKGR IDMDKYEVID IEDGRDDDFN VSMKNAFKLH NKETEEVHLF FAKKLEEKIR WLRAFREERK MVQEDEKIGF EISENQKRQA AMTVRKASKQ KVTQRKWHY

UniProtKB: Isoform 2 of Rho guanine nucleotide exchange factor 9

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.333 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHepes
250.0 mMNaClsodium chloride
2.0 %C12H22O11Sucrose
50.0 mMC6H14N4O2Arginine
50.0 mMC5H10N2O3Glutamate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV
Detailsthe sample was mixed on-grid

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 3 / Number real images: 15966 / Average exposure time: 40.0 sec. / Average electron dose: 31.0 e/Å2 / Details: Calibrated pixel size: 0.862
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

+
Image processing

Particle selectionNumber selected: 445782 / Details: after template picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1+patch 240110) / Software - details: patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1+patch 240110) / Software - details: Non-uniform refinement / Number images used: 78879
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1+patch 240110) / Software - details: Non-uniform refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1+patch 240110) / Software - details: Non-uniform refinement
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.4.1+patch 240110) / Software - details: Ab-initio
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