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Yorodumi- EMDB-41185: Cryo-EM structure of Arabidopsis thaliana Bor1 in lipid nanodiscs... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41185 | |||||||||
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Title | Cryo-EM structure of Arabidopsis thaliana Bor1 in lipid nanodiscs (protomer-focused refinement) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Borate 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 / 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 | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.15 Å | |||||||||
Authors | Jiang Y / Jiang J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
-Downloads & links
-EMDB archive
Map data | EMDB map data format | |||
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Header (meta data) | EMDB header | |||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41185 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41185 | HTTPS FTP |
-Validation report
Summary document | emd_41185_validation.pdf.gz | 833.9 KB | Display | EMDB validaton report |
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Full document | emd_41185_full_validation.pdf.gz | 833.5 KB | Display | |
Data in XML | emd_41185_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | emd_41185_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41185 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41185 | HTTPS FTP |
-Related structure data
Related structure data | 8tegMC 41186 41187 41188 41190 41191 41192 8tehC 8teiC 8tejC 8telC 8temC 8tenC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41185.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Arabidopsis thaliana Boron transporter 1
Entire | Name: Arabidopsis thaliana Boron transporter 1 |
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Components |
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-Supramolecule #1: Arabidopsis thaliana Boron transporter 1
Supramolecule | Name: Arabidopsis thaliana Boron transporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Boron transporter 1
Macromolecule | Name: Boron transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 80.056992 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 HHMQTPLVYQ QPQGLKELKE STIQATTFTG NLNAPVDETL FDIEKEIDDL LPVEVKEQRV SNLLQSTMVG GCVAA MPIL KMIPTSVLWG YFAFMAIESL PGNQFWERIL LLFTAPSRRF KVLEDYHATF VETVPFKTIA MFTLFQTTYL LICFGL TWI PIAGVMFPLM IMFLIPVRQY LLPRFFKGAH LQDLDAAEYE EAPALPFNLA AETEIGSTTS YPGDLEILDE VMTRSRG EF RHTSSPKVTS SSSTPVNNRS LSQVFSPRVS GIRLGQMSPR VVGNSPKPAS CGRSPLNQSS SNHHHHHHHH HH UniProtKB: Boron transporter 1 |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 88 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 853837 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |