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- EMDB-64976: Cryo-EM structure of the aspartate:alanine antiporter AspT WT_SD_... -

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Basic information

Entry
Database: EMDB / ID: EMD-64976
TitleCryo-EM structure of the aspartate:alanine antiporter AspT WT_SD_Local refinement
Map dataThe focused map of SD
Sample
  • Organelle or cellular component: aspartate:alanine antiporter AspT
    • Protein or peptide: Aspartate/alanine antiporter
Keywordsamino acid / antiporter / elevator mechanism / TRANSPORT PROTEIN
Biological speciesTetragenococcus halophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsNanatani K / Kanno R / Kawabata T / Watanabe S / Hidaka M / Yamanaka T / Toda K / Fujiki T / Kunii K / Miyamoto A ...Nanatani K / Kanno R / Kawabata T / Watanabe S / Hidaka M / Yamanaka T / Toda K / Fujiki T / Kunii K / Miyamoto A / Chiba F / Ogasawara S / Murata T / Humbel BM / Inaba K / Mitsuoka K / Guan L / Abe K / Yamamoto M / Koshiba S
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K07653 Japan
Japan Society for the Promotion of Science (JSPS)20K05779 Japan
Japan Society for the Promotion of Science (JSPS)23K05004 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121019 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121038 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure and molecular mechanism of the aspartate:alanine antiporter AspT from Tetragenococcus halophilus
Authors: Nanatani K / Kanno R / Kawabata T / Watanabe S / Hidaka M / Yamanaka T / Toda K / Fujiki T / Kunii K / Miyamoto A / Chiba F / Ogasawara S / Murata T / Humbel BM / Inaba K / Mitsuoka K / Guan ...Authors: Nanatani K / Kanno R / Kawabata T / Watanabe S / Hidaka M / Yamanaka T / Toda K / Fujiki T / Kunii K / Miyamoto A / Chiba F / Ogasawara S / Murata T / Humbel BM / Inaba K / Mitsuoka K / Guan L / Abe K / Yamamoto M / Koshiba S
History
DepositionJun 7, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64976.png

Downloads & links

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Map

FileDownload / File: emd_64976.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe focused map of SD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 216.32 Å		0.85 Å/pix.
x 256 pix.
= 216.32 Å		0.85 Å/pix.
x 256 pix.
= 216.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.584
Minimum - Maximum-2.0079217 - 2.4142196
Average (Standard dev.)0.003691396 (±0.05796545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64976_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_64976_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_64976_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : aspartate:alanine antiporter AspT

EntireName: aspartate:alanine antiporter AspT
Components
  • Organelle or cellular component: aspartate:alanine antiporter AspT
    • Protein or peptide: Aspartate/alanine antiporter

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Supramolecule #1: aspartate:alanine antiporter AspT

SupramoleculeName: aspartate:alanine antiporter AspT / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Tetragenococcus halophilus (bacteria) / Strain: D10
Molecular weightTheoretical: 58 KDa

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Macromolecule #1: Aspartate/alanine antiporter

MacromoleculeName: Aspartate/alanine antiporter / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetragenococcus halophilus (bacteria) / Strain: D10
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNAIGNFLVG TPVFTIFICL ALGYLLGKLK IGSFTLGATV GVLIVALLIG QLGVFPRDTL LGDIFFDFFM FAIGYRVGPS FISSMKKFG AKIVYATLIF LVSAFIVAYA CFKMFHIGPG IAAGIIAGGL TQSAVIGSSL ETISKLPISD HLKTLYSNQI P IVYTLTYV ...String:
MNAIGNFLVG TPVFTIFICL ALGYLLGKLK IGSFTLGATV GVLIVALLIG QLGVFPRDTL LGDIFFDFFM FAIGYRVGPS FISSMKKFG AKIVYATLIF LVSAFIVAYA CFKMFHIGPG IAAGIIAGGL TQSAVIGSSL ETISKLPISD HLKTLYSNQI P IVYTLTYV FGTIGVLIFL RDIMPKLMHI DLKKQAVKTA KELDMIPVPV IVASTHFYTI NDGSSLIGQT LGTVNTKFAK GL VAAGLND SADMASVINA GDVLAISGGI DEIGRAVQEF NLLEVTGKTK AYVSKQVVLK KNFSADVLKN AQDKGVLVAT LAG DVMDPA QFSTLKPAES VTLVGQKDAV SEVQSQLGRL RAAENIINYS WFALGIALSA ALGIVGTKVS GVPIALGGGT ASLI VGLVQ SIYRDKHAHM DTIPDSLLEF FQSIGLNLFI ATVGLSAAKT FISAIQSMGI SVLLIGAVIS ILPHIITFVI CYYLM KMEP ISIIGAQTGA DTLSAALNDV SERVGSDASP FFAAAVAPAY AIGNIFLTLM GPIFIVLLS

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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

Concentration2.83 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4S2-(N-morpholino)ethanesulfonic acid
100.0 mMNaClsodium chloride
0.003 %C47H88O22Lauryl maltose neopentyl glycol
100.0 mMC4H7NO4L-aspartic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 8 / Number real images: 12357 / Average exposure time: 30.6 sec. / Average electron dose: 40.0 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: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 96000
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: 1636712
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 125465
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE

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