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- EMDB-62647: Folate ECF transporter affected by PFOS -

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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 / 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-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62647.png

Downloads & links

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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 °

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Supplemental data

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Half map: #1

Fileemd_62647_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62647_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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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)

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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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

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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

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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)

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