[English] 日本語
Yorodumi
- EMDB-51034: Cryo-EM reconstruction of the full-length E. coli transmembrane f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51034
TitleCryo-EM reconstruction of the full-length E. coli transmembrane formate transporter FocA
Map dataC5 reconstruction of the E. coli transmembrane formate transporter FocA
Sample
  • Complex: C5-symmetric complex of the inner membrane formate transporter FocA
    • Protein or peptide: Formate channel FocA
  • Ligand: water
KeywordsFNT-transporter / FocA / formate / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsTueting C / Janson K / Kyrilis FL / Hamdi F / Kastritis PL
Funding support Germany, European Union, 6 items
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 FL / Hamdi F / Erdmann C / Sinz A / Sawers RG / Kastritis PL
History
DepositionJul 15, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51034.png

Downloads & links

-
Map

FileDownload / File: emd_51034.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC5 reconstruction of the E. coli transmembrane formate transporter FocA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.59 Å/pix.
x 256 pix.
= 151.501 Å		0.59 Å/pix.
x 256 pix.
= 151.501 Å		0.59 Å/pix.
x 256 pix.
= 151.501 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5918 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.57139856 - 0.9708302
Average (Standard dev.)0.0010007003 (±0.051175676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 151.5008 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51034_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Asymmetric reconstruction of the E. coli transmembrane formate...

Fileemd_51034_additional_1.map
AnnotationAsymmetric reconstruction of the E. coli transmembrane formate transporter FocA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: C5 reconstruction of the E. coli transmembrane formate...

Fileemd_51034_half_map_1.map
AnnotationC5 reconstruction of the E. coli transmembrane formate transporter FocA - Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: C5 reconstruction of the E. coli transmembrane formate...

Fileemd_51034_half_map_2.map
AnnotationC5 reconstruction of the E. coli transmembrane formate transporter FocA - Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : C5-symmetric complex of the inner membrane formate transporter FocA

EntireName: C5-symmetric complex of the inner membrane formate transporter FocA
Components
  • Complex: C5-symmetric complex of the inner membrane formate transporter FocA
    • Protein or peptide: Formate channel FocA
  • Ligand: water

-
Supramolecule #1: C5-symmetric complex of the inner membrane formate transporter FocA

SupramoleculeName: C5-symmetric complex of the inner membrane formate transporter FocA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: Formate channel FocA

MacromoleculeName: Formate channel FocA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 31.012605 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MKADNPFDLL LPAAMAKVAE EAGVYKATKH PLKTFYLAIT AGVFISIAFV FYITATTGTG TMPFGMAKLV GGICFSLGLI LCVVCGADL FTSTVLIVVA KASGRITWGQ LAKNWLNVYF GNLVGALLFV LLMWLSGEYM TANGQWGLNV LQTADHKVHH T FIEAVCLG ...String:
MKADNPFDLL LPAAMAKVAE EAGVYKATKH PLKTFYLAIT AGVFISIAFV FYITATTGTG TMPFGMAKLV GGICFSLGLI LCVVCGADL FTSTVLIVVA KASGRITWGQ LAKNWLNVYF GNLVGALLFV LLMWLSGEYM TANGQWGLNV LQTADHKVHH T FIEAVCLG ILANLMVCLA VWMSYSGRSL MDKAFIMVLP VAMFVASGFE HSIANMFMIP MGIVIRDFAS PEFWTAVGSA PE NFSHLTV MNFITDNLIP VTIGNIIGGG LLVGLTYWVI YLRENDHH

UniProtKB: Formate channel FocA

-
Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
Details: Plasma Treated, 25 s Sample Negative, 0.4 mbar pressure, 15 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number real images: 3665 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

DetailsAll acquired movies were motion corrected
Particle selectionNumber selected: 2260127
Details: Particles were picked using Template Picker with a particle diameter of 140 A
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 302937
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3kcv


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe inital model was rigid-fitted using ChimeraX, and refined iteratively using Coot and Phenix
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g49:
Cryo-EM reconstruction of the full-length E. coli transmembrane formate transporter FocA

+
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