8ONT | pdb_00008ont

Structure of Setaria italica NRAT in complex with a nanobody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional properties of a plant NRAMP-related aluminum transporter.

Ramanadane, K.Liziczai, M.Markovic, D.Straub, M.S.Rosalen, G.T.Udovcic, A.Dutzler, R.Manatschal, C.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.85641
  • Primary Citation of Related Structures:  
    8ONT

  • PubMed Abstract: 

    The transport of transition metal ions by members of the SLC11/NRAMP family constitutes a ubiquitous mechanism for the uptake of Fe 2+ and Mn 2+ 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 2+ uptake in prokaryotes and another the transport of Al 3+ into plant cells. Our previous work on the SLC11 transporter from Eggerthella lenta revealed the basis for its Mg 2+ selectivity (Ramanadane et al., 2022). Here, we have addressed the structural and functional properties of a putative Al 3+ transporter from Setaria italica . We show that the protein transports diverse divalent metal ions and binds the trivalent ions Al 3+ and Ga 3+ , 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.


  • Organizational Affiliation
    • Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NRAMP related aluminium transporter552Setaria italicaMutation(s): 0 
Gene Names: 101781512SETIT_1G098100v2
Membrane Entity: Yes 
UniProt
Find proteins for K3YRE7 (Setaria italica)
Explore K3YRE7 
Go to UniProtKB:  K3YRE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK3YRE7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody1122Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLC
Query on PLC

Download Ideal Coordinates CCD File 
C [auth A]DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
Other governmentSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-09
    Changes: Data collection