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- PDB-9g4d: Cryo-EM reconstruction of the full-length H209N mutant E. coli tr... -

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Basic information

Entry
Database: PDB / ID: 9g4d
TitleCryo-EM reconstruction of the full-length H209N mutant E. coli transmembrane formate transporter FocA
ComponentsFormate channel FocA
KeywordsMEMBRANE PROTEIN / FNT-transporter / FocA / formate / H209N
Function / homology
Function and homology information


formate transport / mixed acid fermentation / formate transmembrane transporter activity / response to acidic pH / identical protein binding / plasma membrane
Similarity search - Function
Formate transporter FocA, putative / Formate and nitrite transporters signature 1. / Formate and nitrite transporters signature 2. / Formate/nitrite transporter / Formate/nitrite transporter, conserved site / Formate/nitrite transporter / Aquaporin-like
Similarity search - Domain/homology
Formate channel FocA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsTueting, C. / Janson, K. / Kyrilis, F.L. / Hamdi, F. / Kastritis, P.L.
Funding support Germany, European Union, 6items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research03Z22HN23 Germany
German Federal Ministry for Education and Research03Z22HI2 Germany
German Federal Ministry for Education and Research03COV04 Germany
German Research Foundation (DFG)391498659 Germany
European Regional Development FundEFRE: ZS/2016/04/78115European Union
European Research Council (ERC)101086665European Union
CitationJournal: Nat Commun
Title: Conserved hydrophilic checkpoints tune FocA-mediated formate:H+ symport
Authors: Tueting, C. / Janson, K. / Kammel, M. / Ihling, C. / Kyrilis, F.L. / Hamdi, F. / Erdmann, C. / Sinz, A. / Sawers, R.G. / Kastritis, P.L.
History
DepositionJul 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formate channel FocA


Theoretical massNumber of molelcules
Total (without water)30,9891
Polymers30,9891
Non-polymers00
Water00
1
A: Formate channel FocA
x 5


Theoretical massNumber of molelcules
Total (without water)154,9435
Polymers154,9435
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

#1: Protein Formate channel FocA / Formate transporter FocA


Mass: 30988.562 Da / Num. of mol.: 1 / Mutation: H209N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: focA, ycaE, b0904, JW0887 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AC23
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: C5-symmetric complex of the inner membrane H209N mutant formate transporter FocA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 3665

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4particle selection
2EPUimage acquisition
4cryoSPARC4.4CTF correction
7UCSF ChimeraX1.8model fitting
9Coot0.9.6model refinement
10PHENIX1.12rc1model refinement
13cryoSPARC4.4classification
14cryoSPARC4.43D reconstruction
Image processingDetails: All acquired movies were motion corrected
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1150907
Details: Particles were picked using Template Picker with a particle diameter of 140 A
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348935 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: The inital model was rigid-fitted using ChimeraX, and refined iteratively using Coot and Phenix
Atomic model buildingPDB-ID: 3kcv

3kcv


Pdb chain-ID: A / Accession code: 3kcv / Source name: PDB / Type: experimental model

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