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- EMDB-41188: Cryo-EM structure of Arabidopsis thaliana Bor1 mutant (R637E/E641... -

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Basic information

Entry
Database: EMDB / ID: EMD-41188
TitleCryo-EM structure of Arabidopsis thaliana Bor1 mutant (R637E/E641R/R643E) in the occluded conformation in lauryl maltose neopentyl glycol (LMNG) (protomer-focused refinement)
Map data
Sample
  • Complex: Arabidopsis thaliana Boron transporter 1
    • Protein or peptide: Boron transporter 1
  • Ligand: water
KeywordsBorate transporter / Bor1 / TRANSPORT PROTEIN
Function / homology
Function and homology information


borate transmembrane transport / response to boron-containing substance / cellular response to boron-containing substance levels / active borate transmembrane transporter activity / monoatomic ion homeostasis / solute:inorganic anion antiporter activity / monoatomic anion transport / vacuolar membrane / transmembrane transport / endosome membrane / plasma membrane
Similarity search - Function
Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsJiang Y / Jiang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Structure of borate transporter Bor1 reveals a novel auto-inhibition mechanism for the SLC4 family
Authors: Jiang Y / Jiang J
History
DepositionJul 6, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41188.png

Downloads & links

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Map

FileDownload / File: emd_41188.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05091601 - 0.09724064
Average (Standard dev.)0.000015119674 (±0.0018992099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41188_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_41188_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana Boron transporter 1

EntireName: Arabidopsis thaliana Boron transporter 1
Components
  • Complex: Arabidopsis thaliana Boron transporter 1
    • Protein or peptide: Boron transporter 1
  • Ligand: water

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Supramolecule #1: Arabidopsis thaliana Boron transporter 1

SupramoleculeName: Arabidopsis thaliana Boron transporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Boron transporter 1

MacromoleculeName: Boron transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 80.108898 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MEETFVPFEG IKNDLKGRLM CYKQDWTGGF KAGFRILAPT TYIFFASAIP VISFGEQLER STDGVLTAVQ TLASTAICGM IHSIIGGQP LLILGVAEPT VIMYTFMFNF AKARPELGRD LFLAWSGWVC VWTALMLFVL AICGACSIIN RFTRVAGELF G LLIAMLFM ...String:
MEETFVPFEG IKNDLKGRLM CYKQDWTGGF KAGFRILAPT TYIFFASAIP VISFGEQLER STDGVLTAVQ TLASTAICGM IHSIIGGQP LLILGVAEPT VIMYTFMFNF AKARPELGRD LFLAWSGWVC VWTALMLFVL AICGACSIIN RFTRVAGELF G LLIAMLFM QQAIKGLVDE FRIPERENQK LKEFLPSWRF ANGMFALVLS FGLLLTGLRS RKARSWRYGT GWLRSLIADY GV PLMVLVW TGVSYIPAGD VPKGIPRRLF SPNPWSPGAY GNWTVVKEML DVPIVYIIGA FIPASMIAVL YYFDHSVASQ LAQ QKEFNL RKPSSYHYDL LLLGFLTLMC GLLGVPPSNG VIPQSPMHTK SLATLKYQLL RNRLVATARR SIKTNASLGQ LYDN MQEAY HHMQ(TPO)PLVYQ QPQGLKELKE STIQATTFTG NLNAPVDETL FDIEKEIDDL LPVEVKEQRV SNLLQSTMVG G CVAAMPIL KMIPTSVLWG YFAFMAIESL PGNQFWERIL LLFTAPSRRF KVLEDYHATF VETVPFKTIA MFTLFQTTYL LI CFGLTWI PIAGVMFPLM IMFLIPVRQY LLPRFFKGAH LQDLDAAEYE EAPALPFNLA AETEIGSTTS YPGDLEILDE VMT ESRGRF EHTSSPKVTS SSSTPVNNRS LSQVFSPRVS GIRLGQMSPR VVGNSPKPAS CGRSPLNQSS SNHHHHHHHH HH

UniProtKB: Boron transporter 1

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 22 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 479691
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
FSC plot (resolution estimation)

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