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- EMDB-50069: BasC in complex with nanobody 53 -

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Basic information

Entry
Database: EMDB / ID: EMD-50069
TitleBasC in complex with nanobody 53
Map datamap from Non-Uniform refinement
Sample
  • Complex: BasC in complex with nanobody 53
    • Protein or peptide: BasC
    • Protein or peptide: nanobody 53
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 (mammal)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsFort J / Palacin M
Funding support Spain, 2 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021- 122802OB-I00 Spain
Generalitat de Catalunya2021 SGR 01281 Spain
CitationJournal: To Be Published
Title: BasC in complex with nanobody 71
Authors: Fort J / Nicolas-Arago A / Maggi L / Martinez Molledo M / Kapiki D / Zijlstra N / Bodoy S / Pardon E / Llorca O / Orozco M / Cordes T / Palacin M
History
DepositionApr 10, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50069.png

Downloads & links

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Map

FileDownload / File: emd_50069.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap from Non-Uniform refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.64
Minimum - Maximum-1.5090404 - 3.1630626
Average (Standard dev.)0.0016083262 (±0.060023785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A map from Non-uniform refinement

Fileemd_50069_half_map_1.map
Annotationhalf_A map from Non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map from Non-uniform refinement

Fileemd_50069_half_map_2.map
Annotationhalf_B map from Non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BasC in complex with nanobody 53

EntireName: BasC in complex with nanobody 53
Components
  • Complex: BasC in complex with nanobody 53
    • Protein or peptide: BasC
    • Protein or peptide: nanobody 53

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Supramolecule #1: BasC in complex with nanobody 53

SupramoleculeName: BasC in complex with nanobody 53 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Carnobacterium sp. AT7 (bacteria)
Molecular weightTheoretical: 46 KDa

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Macromolecule #1: BasC

MacromoleculeName: BasC / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Carnobacterium sp. AT7 (bacteria)
SequenceString: MKEVSGITAL TVVVGTVIGA GIFFKPTAVY GAAGAPGLGL LAWFVAGIIT IAGGLTVAEI GTIYPQTGGM MIYLEKVYGR WLGFLVGWAQ MVIYYPANIA ALAIIFATQF VNLFALSDST IVPTAILTSI FLMGVNFLGT KYSGWIQTLA TILKLIPLVV IIVAGLLYPG ...String:
MKEVSGITAL TVVVGTVIGA GIFFKPTAVY GAAGAPGLGL LAWFVAGIIT IAGGLTVAEI GTIYPQTGGM MIYLEKVYGR WLGFLVGWAQ MVIYYPANIA ALAIIFATQF VNLFALSDST IVPTAILTSI FLMGVNFLGT KYSGWIQTLA TILKLIPLVV IIVAGLLYPG GGVIRLVPFS VETHPVLTSF GSALIATLFA YDGWINVGTL AGEMKNPGKM LPKVIIGGLS IVMAVYLLTN IAYLFVLDSS QLAGTDTPAA LVASHLFEGI GSKLVTIGIL ISVFGGINGY IISGLRVPYA LATQKMLPFS DWFARINPKT NLPINGGLVM LGIAIVMILT GQFNQLTDLI VFVIWFFITL TFIAVIILRK TQPDIERPYR VPFYPVIPLI AIIGGLYIIF NTLIVQPKNA FIGILLTLIG IPIYFYCKKK YGSPEGGGLE VLFQ

UniProtKB: Putative amino acid/polyamine transport protein

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Macromolecule #2: nanobody 53

MacromoleculeName: nanobody 53 / type: protein_or_peptide / ID: 2 / Details: nanobody created against BasC / Enantiomer: DEXTRO
Source (natural)Organism: Lama (mammal)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGIAFS RMSMAWYRQD PGKQRALVAR ITNDGSTYYD DSVKGRFTI SRDNAKNTVH LQMNSLKPED TAVYYCNAQL VAWSENYWGQ GTQVTVSSHH H HHHEPEA

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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

Concentration2.9 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: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2642 / Average electron dose: 39.03 e/Å2
Electron beamAcceleration voltage: 200 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: 2.8000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 936733
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6f2g

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: OTHER / Software: (Name: cryoSPARC (ver. v4), RELION (ver. 4.0)) / Details: GSFSC Resolution using Loose mask / Number images used: 87775
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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