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

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Basic information

Entry
Database: PDB / ID: 9gw9
TitleCryo-EM structure of Gephyrin E domain filament interface
ComponentsGephyrin
KeywordsPROTEIN BINDING / Dimer / filament / scaffolding / inhibitory synapse
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMacha, A. / Gunkel, M. / Schwarz, G. / Behrmann, E. / Burdina, N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
Citation
Journal: To Be Published
Title: Cryo-EM structure of Gephyrin E domain filament interface
Authors: Macha, A. / Gunkel, M. / Schwarz, G. / Behrmann, E. / Burdina, N.
#1: Journal: 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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gephyrin
B: Gephyrin
C: Gephyrin


Theoretical massNumber of molelcules
Total (without water)139,9213
Polymers139,9213
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Gephyrin / Putative glycine receptor-tubulin linker protein


Mass: 46640.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Gephyrin E filament interface / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.093 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisC4H11NO31
2250 mMSodium chlorideNaCl1
35 mMMercaptoethanolC2H6OS1
425 mMMonosodiumglutamateC5H8NNaO41
525 mMArgininH2NC(NH)NH(CH2)3CH(NH2)CO2H1
61 %SucroseC12H22O111
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: polydisperse filament
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 43 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6832 / Details: Combined tilted and untilted datasets

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4particle selectionfilament tracer > template picker
2EPU2.12.1.2782RELimage acquisition
4cryoSPARC4.4CTF correctionpatchCTF
7Coot0.9.4model fitting
9cryoSPARC4.4initial Euler assignmentab initio
10cryoSPARC4.4final Euler assignmentnon-uniform refinement
11cryoSPARC4.4classification3D classification
12cryoSPARC4.43D reconstructionnon-uniform refinement
13PHENIX1.21-5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6400000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120264 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: itterative manual building in coot with realspace refinement in phenix
Atomic model buildingPDB-ID: 2FU3

2fu3


Pdb chain-ID: A / Accession code: 2FU3 / Source name: PDB / Type: experimental model

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