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- EMDB-11996: OsBOR3 -

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Basic information

Entry
Database: EMDB / ID: EMD-11996
TitleOsBOR3
Map data
Sample
  • Complex: Borate transporter 3 from Oryza sativa (osBOR3)
    • Protein or peptide: Oryza sativa borate transporter 3
Function / homologyBicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter family / solute:inorganic anion antiporter activity / membrane => GO:0016020 / Boron transporter
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsByrne B / Barritt JD
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N016467/1 United Kingdom
European Commission722687 United Kingdom
CitationJournal: Sci Rep / Year: 2021
Title: Structural and functional insights into the mechanism of action of plant borate transporters.
Authors: Savvas Saouros / Thotegowdanapalya C Mohan / Cristina Cecchetti / Silke Lehmann / Joseph D Barrit / Nicola J Scull / Paul Simpson / Yilmaz Alguel / Alexander D Cameron / Alexandra M E Jones ...Authors: Savvas Saouros / Thotegowdanapalya C Mohan / Cristina Cecchetti / Silke Lehmann / Joseph D Barrit / Nicola J Scull / Paul Simpson / Yilmaz Alguel / Alexander D Cameron / Alexandra M E Jones / Bernadette Byrne /
Abstract: Boron has essential roles in plant growth and development. BOR proteins are key in the active uptake and distribution of boron, and regulation of intracellular boron concentrations. However, their ...Boron has essential roles in plant growth and development. BOR proteins are key in the active uptake and distribution of boron, and regulation of intracellular boron concentrations. However, their mechanism of action remains poorly studied. BOR proteins are homologues of the human SLC4 family of transporters, which includes well studied mammalian transporters such as the human Anion Exchanger 1 (hAE1). Here we generated Arabidopsis thaliana BOR1 (AtBOR1) variants based (i) on known disease causing mutations of hAE1 (S466R, A500R) and (ii) a loss of function mutation (D311A) identified in the yeast BOR protein, ScBOR1p. The AtBOR1 variants express in yeast and localise to the plasma membrane, although both S466R and A500R exhibit lower expression than the WT AtBOR1 and D311A. The D311A, S466R and A500R mutations result in a loss of borate efflux activity in a yeast bor1p knockout strain. A. thaliana plants containing these three individual mutations exhibit substantially decreased growth phenotypes in soil under conditions of low boron. These data confirm an important role for D311 in the function of the protein and show that mutations equivalent to disease-causing mutations in hAE1 have major effects in AtBOR1. We also obtained a low resolution cryo-EM structure of a BOR protein from Oryza sativa, OsBOR3, lacking the 30 C-terminal amino acid residues. This structure confirms the gate and core domain organisation previously observed for related proteins, and is strongly suggestive of an inward facing conformation.
History
DepositionDec 1, 2020-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11996.png

Downloads & links

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Map

FileDownload / File: emd_11996.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.011076495 - 0.03333941
Average (Standard dev.)0.00014402113 (±0.0013053054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 277.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z277.500277.500277.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0110.0330.000

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Supplemental data

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Mask #1

Fileemd_11996_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Borate transporter 3 from Oryza sativa (osBOR3)

EntireName: Borate transporter 3 from Oryza sativa (osBOR3)
Components
  • Complex: Borate transporter 3 from Oryza sativa (osBOR3)
    • Protein or peptide: Oryza sativa borate transporter 3

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Supramolecule #1: Borate transporter 3 from Oryza sativa (osBOR3)

SupramoleculeName: Borate transporter 3 from Oryza sativa (osBOR3) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Homodimer of the osBOR3 integral membrane protein in LMNG detergent belt.
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Oryza sativa borate transporter 3

MacromoleculeName: Oryza sativa borate transporter 3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MEESFVPLRG IKNDLHGRL Q CYKQDWTG GF RAGIRIL APT TYIFFA SAIP VISFG EQLER NTDG VLTAVQ TLA STALCGI IH SFLGGQPL L ILGVAEPTV LMYTFMFNFA KDRPDLGRR L FLAWTGWV CV WTAILLF LLA ILGACS IINR FTRIA ...String:
MEESFVPLRG IKNDLHGRL Q CYKQDWTG GF RAGIRIL APT TYIFFA SAIP VISFG EQLER NTDG VLTAVQ TLA STALCGI IH SFLGGQPL L ILGVAEPTV LMYTFMFNFA KDRPDLGRR L FLAWTGWV CV WTAILLF LLA ILGACS IINR FTRIA GELFG LLIA MLFMQQ AIK GLVDEFR IP ERENRKAL E FVSSWRFAN GMFAIVLSFG LLLTALRSR K ARSWRYGT GW LRGFIAD YGV PLMVLV WTGV SYIPY GSVPK GIPR RLFSPN PWS PGAYDNW TV IRDMPNVP L LYIIGAFIP ATMIAVLYYF DHSVASQLA Q QKEFNLRK PP SFHYDLL LLG FLTLLC GLIG IPPAN GVIPQ SPMH TKSLAT LKH QLLRNRL VA TARQSMSQ N ASLSQLYGS MQEAYQQMQT PLIYQQPSV K GLNELKDS TV QMASSMG NID APVDET VFDI EKEID DLLPI EVKE QRLSNL LQA SMVGGCV AA MPLLKKIP T SVLWGYFAF MAIESLPGNQ FWERILLLF T APSRRYKV LE EYHTTFV ETV PFKTIA MFTL FQTMY LLVCF GITW IPIAGV LFP LMIMLLV PV RQYILPKL F KGAHLTDLD AAEYEESPAI PFIAAQDID V ALARTQSA EI LDDIVTR SRG EI

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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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 20.265 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot time -2 blot force.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6285 / Average exposure time: 4.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2548682
Details: Picked using RELION auto picker with 2D class references generated from manually picked particles.
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Software - details: Estimate CTF parameters
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 91034 / Software - Name: RELION (ver. 3) / Software - details: 3D classification used / Details: Best class contained 156116
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Software - details: 3D refinement / Number images used: 116140
DetailsSuper-resolution movies were binned by a factor of 2 and aligned with MotionCor2 and CTF estimation achieved with CTFFind4.
FSC plot (resolution estimation)

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