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- EMDB-51644: Cryo-EM structure of Gephyrin E domain filament interface -

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Basic information

Entry
Database: EMDB / ID: EMD-51644
TitleCryo-EM structure of Gephyrin E domain filament interface
Map dataGephyrin E domain filament interface - AI sharpened map
Sample
  • Complex: Gephyrin E filament interface
    • Protein or peptide: Gephyrin
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 / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering ...Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / molybdopterin cofactor binding / response to metal ion / postsynaptic specialization, intracellular component / neurotransmitter receptor localization to postsynaptic specialization membrane / protein targeting / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / GABA-ergic synapse / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / molecular adaptor activity / dendritic spine / postsynaptic membrane / cytoskeleton / postsynapse / postsynaptic density / signaling receptor binding / neuronal cell body / dendrite / ATP binding / metal ion binding / identical protein binding / cytosol / cytoplasm
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: 3.6 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 26, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51644.png

Downloads & links

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Map

FileDownload / File: emd_51644.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGephyrin E domain filament interface - AI sharpened map
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: 0.5
Minimum - Maximum-3.0279336 - 4.4642186
Average (Standard dev.)-0.00002356638 (±0.08451639)
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 E domain filament interface - AI sharpened map

Fileemd_51644_additional_1.map
AnnotationGephyrin E domain filament interface - AI sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Gephyrin E domain filament interface - map from odd particles

Fileemd_51644_half_map_1.map
AnnotationGephyrin E domain filament interface - map from odd particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Gephyrin E domain filament interface - map from even particles

Fileemd_51644_half_map_2.map
AnnotationGephyrin E domain filament interface - map from even 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 filament interface

EntireName: Gephyrin E filament interface
Components
  • Complex: Gephyrin E filament interface
    • Protein or peptide: Gephyrin

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Supramolecule #1: Gephyrin E filament interface

SupramoleculeName: Gephyrin E filament interface / 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

MacromoleculeName: Gephyrin / type: protein_or_peptide / ID: 1
Details: The following amino acids were reduced to their respective C-beta atoms: ChainA/ LEU 432 - ILE 447 ChainA/ VAL 574 - ASP 580 ChainB/ VAL 574 - ASP 580 ChainC/ LEU 432 - ILE 447
Number of copies: 3 / Enantiomer: LEVO / EC number: molybdopterin adenylyltransferase
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 46.640352 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRGSHHHHHH GSACELGTDK AFITVLEMTP VLGTEIINYR DGMGRVLAQD VYAKDNLPPF PASVKDGYAV RAADGPGDRF IIGESQAGE QPTQTVMPGQ VMRVTTGAPI PCGADAVVQV EDTELIRESD DGTEELEVRI LVQARPGQDI RPIGHDIKRG E CVLAKGTH ...String:
MRGSHHHHHH GSACELGTDK AFITVLEMTP VLGTEIINYR DGMGRVLAQD VYAKDNLPPF PASVKDGYAV RAADGPGDRF IIGESQAGE QPTQTVMPGQ VMRVTTGAPI PCGADAVVQV 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 statefilament

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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailspolydisperse filament

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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: 6832 / Average exposure time: 43.0 sec. / Average electron dose: 30.0 e/Å2 / Details: Combined tilted and untilted datasets
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: 6400000
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: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: non-uniform refinement / Number images used: 120264
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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Atomic model buiding 1

Initial modelPDB ID:

2fu3


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Detailsitterative manual building in coot with realspace refinement in phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9gw9:
Cryo-EM structure of Gephyrin E domain filament interface

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