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- PDB-8tei: Cryo-EM structure of Arabidopsis thaliana Bor1 in lauryl maltose ... -

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Basic information

Entry
Database: PDB / ID: 8tei
TitleCryo-EM structure of Arabidopsis thaliana Bor1 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 / vacuole / transmembrane transporter activity / transmembrane transport ...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 / vacuole / transmembrane transporter activity / transmembrane transport / membrane => GO:0016020 / endosome / plasma membrane
Similarity search - Function
Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain
Similarity search - Domain/homology
Chem-POV / Boron transporter 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)178,35626
Polymers160,1142
Non-polymers18,24224
Water3,855214
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: 80056.992 Da / Num. of mol.: 2
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
#2: Chemical...
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: #1 / 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
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156604 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029820
ELECTRON MICROSCOPYf_angle_d0.4913164
ELECTRON MICROSCOPYf_dihedral_angle_d20.4491760
ELECTRON MICROSCOPYf_chiral_restr0.0371398
ELECTRON MICROSCOPYf_plane_restr0.0031574

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