[English] 日本語
Yorodumi
- EMDB-62647: Folate ECF transporter affected by PFOS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62647
TitleFolate ECF transporter affected by PFOS
Map data
Sample
  • Complex: Folate ECF transporter affected by PFOS
    • Protein or peptide: Energy-coupling factor transporter ATP-binding protein EcfA1
    • Protein or peptide: Energy-coupling factor transporter ATP-binding protein EcfA2
    • Protein or peptide: Energy-coupling factor transporter transmembrane protein EcfT
    • Protein or peptide: Folate family ECF transporter S component
KeywordsATPase / Folate transport / HYDROLASE/TRANSPORT PROTEIN / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Translocases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / ECF transporter S component, folate family / ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. ...: / ECF transporter S component, folate family / ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. / : / ABC transporter, CbiO/EcfA subunit / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Energy-coupling factor transporter ATP-binding protein EcfA1 / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter transmembrane protein EcfT / Folate family ECF transporter S component
Similarity search - Component
Biological speciesLevilactobacillus brevis ATCC 367 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsGao Y / Wang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)41925029 China
CitationJournal: To Be Published
Title: First Cryo-EM Structural Observation on the Interaction of Folate ECF Transporter with Perfluoroalkyl Substances
Authors: Wang Z / Li H / Gao Y
History
DepositionDec 9, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62647.png

Downloads & links

-
Map

FileDownload / File: emd_62647.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 280 pix.
= 246.4 Å		0.88 Å/pix.
x 280 pix.
= 246.4 Å		0.88 Å/pix.
x 280 pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0671
Minimum - Maximum-0.33867067 - 0.5259335
Average (Standard dev.)0.0014380643 (±0.016967406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 246.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_62647_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62647_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Folate ECF transporter affected by PFOS

EntireName: Folate ECF transporter affected by PFOS
Components
  • Complex: Folate ECF transporter affected by PFOS
    • Protein or peptide: Energy-coupling factor transporter ATP-binding protein EcfA1
    • Protein or peptide: Energy-coupling factor transporter ATP-binding protein EcfA2
    • Protein or peptide: Energy-coupling factor transporter transmembrane protein EcfT
    • Protein or peptide: Folate family ECF transporter S component

-
Supramolecule #1: Folate ECF transporter affected by PFOS

SupramoleculeName: Folate ECF transporter affected by PFOS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Levilactobacillus brevis ATCC 367 (bacteria)

-
Macromolecule #1: Energy-coupling factor transporter ATP-binding protein EcfA1

MacromoleculeName: Energy-coupling factor transporter ATP-binding protein EcfA1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Translocases
Source (natural)Organism: Levilactobacillus brevis ATCC 367 (bacteria)
Molecular weightTheoretical: 30.419234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TENIISVDHL TYQYDENQAP ALTDVSFTVH AGEWLAIVGH NGSGKSTLAK SLDGLLPFTQ GSVTVGGITL TPETVWQVRE QIGMIFQNP DNQFVGATVE DDVAFGLENR QISRDEMVPR VQAALAQVGM TSFAQREPSS LSGGQKQRVA LAGIVAIAPK I LILDEATS ...String:
TENIISVDHL TYQYDENQAP ALTDVSFTVH AGEWLAIVGH NGSGKSTLAK SLDGLLPFTQ GSVTVGGITL TPETVWQVRE QIGMIFQNP DNQFVGATVE DDVAFGLENR QISRDEMVPR VQAALAQVGM TSFAQREPSS LSGGQKQRVA LAGIVAIAPK I LILDEATS MLDPQGRIEM LAIVRQLRQQ QNLTVISITH DIDEAASADR VLVIDDGRLV DEAVPSQIFE RGTQLVEMGL DL PFTEKLK AALRQRGITP PTTYQTAAEM EEWLWQSLSN T

UniProtKB: Energy-coupling factor transporter ATP-binding protein EcfA1

-
Macromolecule #2: Energy-coupling factor transporter ATP-binding protein EcfA2

MacromoleculeName: Energy-coupling factor transporter ATP-binding protein EcfA2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Levilactobacillus brevis ATCC 367 (bacteria)
Molecular weightTheoretical: 32.045338 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AIAFEHVTYT YQAGTPMAHT ALTDVSLTVP DRGYLAIIGH TGSGKSTLIQ QLNALLKPTS GTIKIDEFTI TPETTNAALK PLRQHVGMV FQFPENQLFE ETVRQDIAFG PKNFGMADAD ALALADEMLT TVGLDQSYAE RSPFELSGGQ MRRVAIAGVL A MQPKVLVL ...String:
AIAFEHVTYT YQAGTPMAHT ALTDVSLTVP DRGYLAIIGH TGSGKSTLIQ QLNALLKPTS GTIKIDEFTI TPETTNAALK PLRQHVGMV FQFPENQLFE ETVRQDIAFG PKNFGMADAD ALALADEMLT TVGLDQSYAE RSPFELSGGQ MRRVAIAGVL A MQPKVLVL DEPTAGLDPQ GRQEMMRLFA RLHQEQGLTI VLVTHQMEDV AQYAEQVAVM HEGRLMKFGT PADVFSNREW LQ DHQLDVP QAAQFARRLR DRGLTFPKQP LTADQLADYL AQQWAQRGAD HV

UniProtKB: Energy-coupling factor transporter ATP-binding protein EcfA2

-
Macromolecule #3: Energy-coupling factor transporter transmembrane protein EcfT

MacromoleculeName: Energy-coupling factor transporter transmembrane protein EcfT
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Levilactobacillus brevis ATCC 367 (bacteria)
Molecular weightTheoretical: 30.321086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNFIFGRYL PLDSVVHRLD PRAKLMLSFC YIIVVFLANN IWSYAILIAF TVGAILSSKI SLGFFLKGIR PLLWLIVFTV VLQLLFSPA GGHTYFHWAF INVTQDGLIN AGYIFVRFLL IIMMSTLLTL STQPLDIATG LASLMKPLRW VKVPVDTLAM M LSIALRFV ...String:
MSNFIFGRYL PLDSVVHRLD PRAKLMLSFC YIIVVFLANN IWSYAILIAF TVGAILSSKI SLGFFLKGIR PLLWLIVFTV VLQLLFSPA GGHTYFHWAF INVTQDGLIN AGYIFVRFLL IIMMSTLLTL STQPLDIATG LASLMKPLRW VKVPVDTLAM M LSIALRFV PTLMDEATKI MNAQRARGVD FGEGGLFKQA KSLIPLMVPL FMSAFNRAED LSTAMEARGY QDSEHRSQYR IL TWQRRDT VTWLLFLLGF VAILIFRHW

UniProtKB: Energy-coupling factor transporter transmembrane protein EcfT

-
Macromolecule #4: Folate family ECF transporter S component

MacromoleculeName: Folate family ECF transporter S component / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Levilactobacillus brevis ATCC 367 (bacteria)
Molecular weightTheoretical: 19.82307 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKTMAKTQLP KLDTLSMVTM GVLMALQLVI SRFSVGNNFI KVSFTFLIVA LIAKWFGPWW GMLTAAVVDV IGTLMTGGPF FIGFTVSAV LGSLIYAVFL YRQPVSWWRV IGASVLIALL VNTLLNTLWV TIMYQTPFWS LLPVRALKEL IVTPVQIVLV Y LLLKSQVI QMIQARLNK

UniProtKB: Folate family ECF transporter S component

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 30 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 400650
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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