+Open data
-Basic information
Entry | Database: PDB / ID: 8ont | |||||||||
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Title | Structure of Setaria italica NRAT in complex with a nanobody | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / NRAT / NRAMP / SLC11 / Metal uptake / Aluminium transporter | |||||||||
Function / homology | Function and homology information aluminum ion transmembrane transporter activity / aluminum cation transport / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / response to aluminum ion / plasma membrane Similarity search - Function | |||||||||
Biological species | Setaria italica (foxtail millet) Lama glama (llama) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
Authors | Ramanadane, K. / Liziczai, M. / Markovic, D. / Straub, M.S. / Rosalen, G.T. / Udovcic, A. / Dutzler, R. / Manatschal, C. | |||||||||
Funding support | Switzerland, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ont.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ont.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ont.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ont_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ont_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ont_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 8ont_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/8ont ftp://data.pdbj.org/pub/pdb/validation_reports/on/8ont | HTTPS FTP |
-Related structure data
Related structure data | 17000MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 60147.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Setaria italica (foxtail millet) / Gene: 101781512, SETIT_1G098100v2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: K3YRE7 |
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#2: Antibody | Mass: 13071.546 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Cell (production host): MC1061 / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-PLC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex between SiNRAT and a nanobody used as a fiducial marker for structure determination Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||
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Molecular weight |
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Source (natural) | Organism: Setaria italica (foxtail millet) | |||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 | |||||||||
Buffer solution | pH: 7 | |||||||||
Specimen | Conc.: 2.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 69.68 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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