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Open data
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Basic information
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Title | Structure of Setaria italica NRAT in complex with a nanobody | |||||||||
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![]() | 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 / manganese ion transmembrane transporter activity / cadmium ion transmembrane transporter activity / response to aluminum ion / plasma membrane / Uncharacterized protein![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
![]() | Ramanadane K / Liziczai M / Markovic D / Straub MS / Rosalen GT / Udovcic A / Dutzler R / Manatschal C | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 11.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.7 KB 16.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.4 KB | Display | ![]() |
Images | ![]() | 105.1 KB | ||
Masks | ![]() | 22.2 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 20.7 MB 20.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 746.7 KB | Display | ![]() |
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Full document | ![]() | 746.2 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ontMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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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
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Density Histograms |
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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: ![]() |
-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: ![]() |
Molecular weight | Theoretical: 60.147227 KDa |
Recombinant expression | Organism: ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 13.071546 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |