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- EMDB-50021: BasC in complex with nanobody 71 -

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Basic information

Entry
Database: EMDB / ID: EMD-50021
TitleBasC in complex with nanobody 71
Map dataSharpened map
Sample
  • Complex: BasC in complex with nanobody 71
    • Protein or peptide: BasC
    • Protein or peptide: Nanobody 71 (nb71)
KeywordsTransporter / nanobody / aminoacid transporter / MEMBRANE PROTEIN
Function / homology: / L-amino acid transmembrane transporter activity / Amino acid/polyamine transporter I / Amino acid permease / membrane / Putative amino acid/polyamine transport protein
Function and homology information
Biological speciesCarnobacterium sp. AT7 (bacteria) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsMartinez Molledo M / Fort J / Palacin M / Llorca O
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021- 122802OB-I00 Spain
Other government2021 SGR 01281 Spain
CitationJournal: PNAS Nexus / Year: 2025
Title: The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the L-amino acid transporters.
Authors: Joana Fort / Adrià Nicolàs-Aragó / Luca Maggi / Maria Martinez-Molledo / Despoina Kapiki / Paula González-Novoa / Patricia Gómez-Gejo / Niels Zijlstra / Susanna Bodoy / Els Pardon / Jan ...Authors: Joana Fort / Adrià Nicolàs-Aragó / Luca Maggi / Maria Martinez-Molledo / Despoina Kapiki / Paula González-Novoa / Patricia Gómez-Gejo / Niels Zijlstra / Susanna Bodoy / Els Pardon / Jan Steyaert / Oscar Llorca / Modesto Orozco / Thorben Cordes / Manuel Palacín /
Abstract: L-Amino acid transporters (LATs) play a key role in a wide range of physiological processes. Defects in LATs can lead to neurological disorders and aminoacidurias, while the overexpression of these ...L-Amino acid transporters (LATs) play a key role in a wide range of physiological processes. Defects in LATs can lead to neurological disorders and aminoacidurias, while the overexpression of these transporters is related to cancer. BasC is a bacterial LAT transporter with an APC fold. In this study, to monitor the cytoplasmic motion of BasC, we developed a single-molecule Förster resonance energy transfer assay that can characterize the conformational states of the intracellular gate in solution at room temperature. Based on combined biochemical and biophysical data and molecular dynamics simulations, we propose a model in which the conserved lysine residue in TM5 supports TM1a to explore both open and closed states within the cytoplasmic gate under apo conditions. This equilibrium can be altered by substrates, mutation of conserved lysine 154 in TM5, or a transport-blocking nanobody interacting with TM1a. Overall, these findings provide insights into the transport mechanism of BasC and highlight the significance of the lysine residue in TM5 in the cytoplasmic gating of LATs.
History
DepositionApr 4, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50021.png

Downloads & links

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Map

FileDownload / File: emd_50021.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.82 Å/pix.
x 120 pix.
= 218.4 Å		1.82 Å/pix.
x 120 pix.
= 218.4 Å		1.82 Å/pix.
x 120 pix.
= 218.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-8.007402000000001 - 14.73302
Average (Standard dev.)0.008002341 (±0.33173755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 218.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50021_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50021_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50021_half_map_2.map
Projections & Slices
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Sample components

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Entire : BasC in complex with nanobody 71

EntireName: BasC in complex with nanobody 71
Components
  • Complex: BasC in complex with nanobody 71
    • Protein or peptide: BasC
    • Protein or peptide: Nanobody 71 (nb71)

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Supramolecule #1: BasC in complex with nanobody 71

SupramoleculeName: BasC in complex with nanobody 71 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Carnobacterium sp. AT7 (bacteria)

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Macromolecule #1: BasC

MacromoleculeName: BasC / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Carnobacterium sp. AT7 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKEVSGITA LTVVVGTVIG AGIFFKPTAV YGAAGAPGLG LLAWFVAGII TIAGGLTVAE I GTIYPQTG GMMIYLEKVY GRWLGFLVGW AQMVIYYPAN IAALAIIFAT QFVNLFALSD ST IVPTAIL TSIFLMGVNF LGTKYSGWIQ TLATILKLIP LVVIIVAGLL ...String:
MKKEVSGITA LTVVVGTVIG AGIFFKPTAV YGAAGAPGLG LLAWFVAGII TIAGGLTVAE I GTIYPQTG GMMIYLEKVY GRWLGFLVGW AQMVIYYPAN IAALAIIFAT QFVNLFALSD ST IVPTAIL TSIFLMGVNF LGTKYSGWIQ TLATILKLIP LVVIIVAGLL YPGGGVIRLV PFS VETHPV LTSFGSALIA TLFAYDGWIN VGTLAGEMKN PGKMLPKVII GGLSIVMAVY LLTN IAYLF VLDSSQLAGT DTPAALVASH LFEGIGSKLV TIGILISVFG GINGYIISGL RVPYA LATQ KMLPFSDWFA RINPKTNLPI NGGLVMLGIA IVMILTGQFN QLTDLIVFVI WFFITL TFI AVIILRKTQP DIERPYRVPF YPVIPLIAII GGLYIIFNTL IVQPKNAFIG ILLTLIG IP IYFYCKKKYG SPE

UniProtKB: Putative amino acid/polyamine transport protein

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Macromolecule #2: Nanobody 71 (nb71)

MacromoleculeName: Nanobody 71 (nb71) / type: protein_or_peptide / ID: 2 / Details: His-tag and EPEA-tag at C-terminus / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAQVQLVESG GGLVQAGGSL RLSCAASSDI FTITAMGWYR QAPGKQRELV ASITSGGRKN YADSVKGRFT ISSDNAKKTV NLQMNSLEPE DTAVYYCHVN YRPLISLDIF DAWGQGTQVT VSSHHHHHHE PEA

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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

Concentration2.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMNH2C(CH2OH)32-Amino-2-(hidroximetil)-1,3-propanodiol, Base tris
0.17 %C22H42O11n-Decyl-beta-D-Maltoside, DM
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 100.0 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 6756 / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 590169
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6f2g

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 169672
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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