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- EMDB-17000: Structure of Setaria italica NRAT in complex with a nanobody -

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Basic information

Entry
Database: EMDB / ID: EMD-17000
TitleStructure of Setaria italica NRAT in complex with a nanobody
Map data
Sample
  • Complex: Complex between SiNRAT and a nanobody used as a fiducial marker for structure determination
    • Protein or peptide: NRAMP related aluminium transporter
    • Protein or peptide: Nanobody1
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: water
KeywordsNRAT / NRAMP / SLC11 / Metal uptake / Aluminium transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


aluminum ion transmembrane transporter activity / aluminum cation transport / metal ion transmembrane transporter activity / manganese ion transport / intracellular manganese ion homeostasis / response to aluminum ion / iron ion transmembrane transport / intracellular iron ion homeostasis / plasma membrane
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like
Similarity search - Domain/homology
Biological speciesSetaria italica (foxtail millet) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsRamanadane K / Liziczai M / Markovic D / Straub MS / Rosalen GT / Udovcic A / Dutzler R / Manatschal C
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Other government Switzerland
CitationJournal: 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
DepositionApr 3, 2023-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17000.png

Downloads & links

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Map

FileDownload / File: emd_17000.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 180 pix.
= 234.36 Å		1.3 Å/pix.
x 180 pix.
= 234.36 Å		1.3 Å/pix.
x 180 pix.
= 234.36 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.355
Minimum - Maximum-3.2556012 - 3.80419
Average (Standard dev.)0.00017259609 (±0.06327917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 234.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17000_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_17000_half_map_1.map
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Half map: #1

Fileemd_17000_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex between SiNRAT and a nanobody used as a fiducial marker f...

EntireName: Complex between SiNRAT and a nanobody used as a fiducial marker for structure determination
Components
  • Complex: Complex between SiNRAT and a nanobody used as a fiducial marker for structure determination
    • Protein or peptide: NRAMP related aluminium transporter
    • Protein or peptide: Nanobody1
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: water

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Supramolecule #1: Complex between SiNRAT and a nanobody used as a fiducial marker f...

SupramoleculeName: Complex between SiNRAT and a nanobody used as a fiducial marker for structure determination
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Setaria italica (foxtail millet)

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Macromolecule #1: NRAMP related aluminium transporter

MacromoleculeName: NRAMP related aluminium transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Setaria italica (foxtail millet)
Molecular weightTheoretical: 60.147227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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: Metal transporter

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Macromolecule #2: Nanobody1

MacromoleculeName: Nanobody1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.071546 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QWQLVESGGG LVQAGGSLRL SCVGSGRAFS SGAMGWFRQT PGQEREFVAA ISWSGGSTVY AESVKGRFTI SMDNAKNTVY LRMNSLQPE DTAVYYCAAG TSTFALRRSP EYWGKGTPVT VSS

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Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.7 mg/mL
BufferpH: 7
GridModel: 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.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5m94

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 300000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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