+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17000 | |||||||||
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Title | Structure of Setaria italica NRAT in complex with a nanobody | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NRAT / NRAMP / SLC11 / Metal uptake / Aluminium transporter / TRANSPORT PROTEIN | |||||||||
Function / homology | aluminum ion transmembrane transporter activity / aluminum cation transport / NRAMP family / Natural resistance-associated macrophage protein-like / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / response to aluminum ion / plasma membrane / Uncharacterized protein Function and homology information | |||||||||
Biological species | Setaria italica (foxtail millet) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
Authors | Ramanadane K / Liziczai M / Markovic D / Straub MS / Rosalen GT / Udovcic A / Dutzler R / Manatschal C | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: Elife / Year: 2023 Title: Structural and functional properties of a plant NRAMP-related aluminum transporter. Authors: Karthik Ramanadane / Márton Liziczai / Dragana Markovic / Monique S Straub / Gian T Rosalen / Anto Udovcic / Raimund Dutzler / Cristina Manatschal / Abstract: The transport of transition metal ions by members of the SLC11/NRAMP family constitutes a ubiquitous mechanism for the uptake of Fe and Mn across all kingdoms of life. Despite the strong conservation ...The transport of transition metal ions by members of the SLC11/NRAMP family constitutes a ubiquitous mechanism for the uptake of Fe and Mn across all kingdoms of life. Despite the strong conservation of the family, two of its branches have evolved a distinct substrate preference with one mediating Mg uptake in prokaryotes and another the transport of Al into plant cells. Our previous work on the SLC11 transporter from revealed the basis for its Mg selectivity (Ramanadane et al., 2022). Here, we have addressed the structural and functional properties of a putative Al transporter from . We show that the protein transports diverse divalent metal ions and binds the trivalent ions Al and Ga, which are both presumable substrates. Its cryo-electron microscopy (cryo-EM) structure displays an occluded conformation that is closer to an inward- than an outward-facing state, with a binding site that is remodeled to accommodate the increased charge density of its transported substrate. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17000.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-17000-v30.xml emd-17000.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17000_fsc.xml | 7.4 KB | Display | FSC data file |
Images | emd_17000.png | 105.1 KB | ||
Masks | emd_17000_msk_1.map | 22.2 MB | Mask map | |
Filedesc metadata | emd-17000.cif.gz | 6.2 KB | ||
Others | emd_17000_half_map_1.map.gz emd_17000_half_map_2.map.gz | 20.7 MB 20.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17000 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17000 | HTTPS FTP |
-Validation report
Summary document | emd_17000_validation.pdf.gz | 746.7 KB | Display | EMDB validaton report |
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Full document | emd_17000_full_validation.pdf.gz | 746.2 KB | Display | |
Data in XML | emd_17000_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_17000_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17000 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17000 | HTTPS FTP |
-Related structure data
Related structure data | 8ontMC M: atomic model generated by this map C: citing same article (ref.) |
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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_17000.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.302 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17000_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17000_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17000_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex between SiNRAT and a nanobody used as a fiducial marker f...
Entire | Name: Complex between SiNRAT and a nanobody used as a fiducial marker for structure determination |
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Components |
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-Supramolecule #1: Complex between SiNRAT and a nanobody used as a fiducial marker f...
Supramolecule | Name: Complex between SiNRAT and a nanobody used as a fiducial marker for structure determination type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Setaria italica (foxtail millet) |
-Macromolecule #1: NRAMP related aluminium transporter
Macromolecule | Name: NRAMP related aluminium transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Setaria italica (foxtail millet) |
Molecular weight | Theoretical: 60.147227 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSERAREVGE TGREARHGVL QSGSDTGDHK DKTVELEKDE QFQGQPKWRK FLAHVGPGAL VAIGFLDPSN LETDMQAGAD FKYELLWVV LVGMIFALLI QTLAANLGVK TGRHLAELCR EEYPRYVNIC LWIIAELAVI SDDIPEVLGT AFAFNILLKI P VWAGVILT ...String: MSERAREVGE TGREARHGVL QSGSDTGDHK DKTVELEKDE QFQGQPKWRK FLAHVGPGAL VAIGFLDPSN LETDMQAGAD FKYELLWVV LVGMIFALLI QTLAANLGVK TGRHLAELCR EEYPRYVNIC LWIIAELAVI SDDIPEVLGT AFAFNILLKI P VWAGVILT VFSTLLLLGV QRFGARKLEF IIAAFMFTMA ACFFGELSYL RPSAKEVVKG MFVPSLQGKG AAANAIALFG AI ITPYNLF LHSALVLSRK TPRSVKSIRA ACRYFLIECS LAFIVAFLIN VSVVVVAGTI CNADNLSPTD SNTCSDLTLQ SAP MLLRNV LGRSSSVVYA VALLASGQST TISCTFAGQV IMQGFLDMKM KNWVRNLITR VIAIAPSLIV SIVSGPSGAG KLII FSSMV LSFEMPFALI PLLKFCNSSK KVGPLKESIY TVVIAWILSF ALIVVNTYFL VWTYVDWLVH NHLPKYANAL VSIVV FALM AAYLVFVVYL TFRRDTVSTY VPVSERAQGQ VEAGGAQAVA SAADADQPAP FRKDLADASM ALEVLFQG UniProtKB: Uncharacterized protein |
-Macromolecule #2: Nanobody1
Macromolecule | Name: Nanobody1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 13.071546 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QWQLVESGGG LVQAGGSLRL SCVGSGRAFS SGAMGWFRQT PGQEREFVAA ISWSGGSTVY AESVKGRFTI SMDNAKNTVY LRMNSLQPE DTAVYYCAAG TSTFALRRSP EYWGKGTPVT VSS |
-Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE
Macromolecule | Name: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PLC |
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Molecular weight | Theoretical: 622.834 Da |
Chemical component information | ChemComp-PLC: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 1 / 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
Concentration | 2.7 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.68 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |