[English] 日本語
Yorodumi
- EMDB-11996: OsBOR3 -

+
Open data


ID or keywords:

Loading...

-
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 integral membrane domain / solute:inorganic anion antiporter activity / monoatomic anion transport / membrane / 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

-
Structure visualization

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

emd_11996.png

Downloads & links

-
Map

FileDownload / File: emd_11996.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 250 pix.
= 277.5 Å		1.11 Å/pix.
x 250 pix.
= 277.5 Å		1.11 Å/pix.
x 250 pix.
= 277.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Mask #1

Fileemd_11996_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Electron beamAcceleration voltage: 300 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsSuper-resolution movies were binned by a factor of 2 and aligned with MotionCor2 and CTF estimation achieved with CTFFind4.
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
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 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
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more