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- PDB-8tem: Cryo-EM structure of Arabidopsis thaliana Bor1 mutant (R637E/E641... -

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Basic information

Entry
Database: PDB / ID: 8tem
TitleCryo-EM structure of Arabidopsis thaliana Bor1 mutant (R637E/E641R/R643E) in the inward-facing conformation in lauryl maltose neopentyl glycol (LMNG)
ComponentsBoron transporter 1
KeywordsTRANSPORT PROTEIN / Borate transporter / Bor1
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsJiang, Y. / Jiang, J.
Funding support United States, 1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary / Category: em_admin / pdbx_entry_details / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Boron transporter 1
B: Boron transporter 1


Theoretical massNumber of molelcules
Total (without water)160,2182
Polymers160,2182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Boron transporter 1


Mass: 80108.898 Da / Num. of mol.: 2 / Fragment: R637E/E641R/R643E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BOR1, At2g47160, T3D7.3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q8VYR7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabidopsis thaliana Boron transporter 1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
9PHENIXmodel refinement
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80443 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038218
ELECTRON MICROSCOPYf_angle_d0.53611164
ELECTRON MICROSCOPYf_dihedral_angle_d3.5961084
ELECTRON MICROSCOPYf_chiral_restr0.0381260
ELECTRON MICROSCOPYf_plane_restr0.0041380

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