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- EMDB-52405: Gephyrin E-domain dimer with additional density on the side of th... -

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Basic information

Entry
Database: EMDB / ID: EMD-52405
TitleGephyrin E-domain dimer with additional density on the side of the dimer interface
Map dataGephyrin with side density
Sample
  • Complex: Gephyrin E-domain dimer with additional density on the side of the dimer interface
    • Complex: Gephyrin dimer
      • Protein or peptide: Gephyrin
    • 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: 4.07 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

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Structure visualization

Supplemental images

emd_52405.png

Downloads & links

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Map

FileDownload / File: emd_52405.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGephyrin with side density
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258.6 Å		0.86 Å/pix.
x 300 pix.
= 258.6 Å		0.86 Å/pix.
x 300 pix.
= 258.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.202
Minimum - Maximum-1.6073864 - 1.9798762
Average (Standard dev.)-0.000042351498 (±0.033507224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Gephyrin with side density, deepEMhancer, sharpened version

Fileemd_52405_additional_1.map
AnnotationGephyrin with side density, deepEMhancer, sharpened version
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Gephyrin with side density, even particles

Fileemd_52405_half_map_1.map
AnnotationGephyrin with side density, even particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Gephyrin with side density, odd particles

Fileemd_52405_half_map_2.map
AnnotationGephyrin with side density, odd particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gephyrin E-domain dimer with additional density on the side of th...

EntireName: Gephyrin E-domain dimer with additional density on the side of the dimer interface
Components
  • Complex: Gephyrin E-domain dimer with additional density on the side of the dimer interface
    • Complex: Gephyrin dimer
      • Protein or peptide: Gephyrin
    • Protein or peptide: Collybistin 2 (-SH3)

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Supramolecule #1: Gephyrin E-domain dimer with additional density on the side of th...

SupramoleculeName: Gephyrin E-domain dimer with additional density on the side of the dimer interface
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 102 KDa

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Supramolecule #2: Gephyrin dimer

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

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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

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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

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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

Concentration0.333 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

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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: 2 / Number real images: 13149 / 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

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Image processing

Particle selectionNumber selected: 210122 / 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: 4.07 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: 62458
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: Heterogeneous refinement
FSC plot (resolution estimation)

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