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- EMDB-50238: Human NRAMP1 (SLC11A1) in an occluded state -

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Basic information

Entry
Database: EMDB / ID: EMD-50238
TitleHuman NRAMP1 (SLC11A1) in an occluded state
Map data
Sample
  • Complex: NRAMP1
    • Protein or peptide: Natural resistance-associated macrophage protein 1
KeywordsIron transport / Manganese transport / Transition metal transport / Divalent metal transport / Metal transport / Transporter / Membrane protein / SLC / Iron uptake / Iron homeostasis / LeuT fold / Small membrane protein / TRANSPORT PROTEIN / NRAMP
Function / homology
Function and homology information


metal cation:proton antiporter activity / transition metal ion transmembrane transporter activity / nitrite transport / L-arginine transmembrane transport / cellular detoxification of cadmium ion / MHC class II biosynthetic process / cadmium ion transmembrane transport / Metal ion SLC transporters / Ion influx/efflux at host-pathogen interface / positive regulation of dendritic cell antigen processing and presentation ...metal cation:proton antiporter activity / transition metal ion transmembrane transporter activity / nitrite transport / L-arginine transmembrane transport / cellular detoxification of cadmium ion / MHC class II biosynthetic process / cadmium ion transmembrane transport / Metal ion SLC transporters / Ion influx/efflux at host-pathogen interface / positive regulation of dendritic cell antigen processing and presentation / manganese ion transport / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / positive regulation of T-helper 1 type immune response / iron ion transmembrane transporter activity / metal ion transport / iron ion transmembrane transport / antigen processing and presentation of peptide antigen / respiratory burst / macrophage activation / ROS and RNS production in phagocytes / antimicrobial humoral response / vacuolar acidification / mRNA stabilization / negative regulation of cytokine production / defense response to protozoan / tertiary granule membrane / T cell proliferation involved in immune response / ficolin-1-rich granule membrane / response to type II interferon / phagocytosis / positive regulation of phagocytosis / cell redox homeostasis / positive regulation of cytokine production / establishment of localization in cell / response to bacterium / wound healing / multicellular organismal-level iron ion homeostasis / positive regulation of type II interferon production / phagocytic vesicle membrane / late endosome membrane / late endosome / iron ion transport / defense response to Gram-negative bacterium / response to lipopolysaccharide / intracellular iron ion homeostasis / lysosome / endosome membrane / defense response to bacterium / inflammatory response / lysosomal membrane / Neutrophil degranulation / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like
Similarity search - Domain/homology
Natural resistance-associated macrophage protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLiziczai M / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for metal ion transport by the human SLC11 proteins DMT1 and NRAMP1.
Authors: Márton Liziczai / Ariane Fuchs / Cristina Manatschal / Raimund Dutzler /
Abstract: Iron and manganese are essential nutrients whose transport across membranes is catalyzed by members of the SLC11 family. In humans, this protein family contains two paralogs, the ubiquitously ...Iron and manganese are essential nutrients whose transport across membranes is catalyzed by members of the SLC11 family. In humans, this protein family contains two paralogs, the ubiquitously expressed DMT1, which is involved in the uptake and distribution of Fe and Mn, and NRAMP1, which participates in the resistance against infections and nutrient recycling. Despite previous studies contributing to our mechanistic understanding of the family, the structures of human SLC11 proteins and their relationship to functional properties have remained elusive. Here we describe the cryo-electron microscopy structures of DMT1 and NRAMP1 and relate them to their functional properties. We show that both proteins catalyze selective metal ion transport coupled to the symport of H, but additionally also mediate uncoupled H flux. Their structures, while sharing general properties with known prokaryotic homologs, display distinct features that lead to stronger transition metal ion selectivity.
History
DepositionMay 2, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50238.png

Downloads & links

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Map

FileDownload / File: emd_50238.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 192 pix.
= 249.984 Å		1.3 Å/pix.
x 192 pix.
= 249.984 Å		1.3 Å/pix.
x 192 pix.
= 249.984 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
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Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.42551053 - 0.8276341
Average (Standard dev.)0.00066898944 (±0.022423012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 249.98401 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50238_msk_1.map
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Half map: #2

Fileemd_50238_half_map_1.map
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Half map: #1

Fileemd_50238_half_map_2.map
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Sample components

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Entire : NRAMP1

EntireName: NRAMP1
Components
  • Complex: NRAMP1
    • Protein or peptide: Natural resistance-associated macrophage protein 1

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Supramolecule #1: NRAMP1

SupramoleculeName: NRAMP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.7 kDa/nm

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Macromolecule #1: Natural resistance-associated macrophage protein 1

MacromoleculeName: Natural resistance-associated macrophage protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.100828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTGDKGPQR LSGSSYGSIS SPTSPTSPGP QQAPPRETYL SEKIPIPDTK PGTFSLRKLW AFTGPGFLMS IAFLDPGNIE SDLQAGAVA GFKLLWVLLW ATVLGLLCQR LAARLGVVTG KDLGEVCHLY YPKVPRTVLW LTIELAIVGS DMQEVIGTAI A FNLLSAGR ...String:
MSTGDKGPQR LSGSSYGSIS SPTSPTSPGP QQAPPRETYL SEKIPIPDTK PGTFSLRKLW AFTGPGFLMS IAFLDPGNIE SDLQAGAVA GFKLLWVLLW ATVLGLLCQR LAARLGVVTG KDLGEVCHLY YPKVPRTVLW LTIELAIVGS DMQEVIGTAI A FNLLSAGR IPLWGGVLIT IVDTFFFLFL DNYGLRKLEA FFGLLITIMA LTFGYEYVVA RPEQGALLRG LFLPSCPGCG HP ELLQAVG IVGAIIMPHN IYLHSALVKS REIDRARRAD IREANMYFLI EATIALSVSF IINLFVMAVF GQAFYQKTNQ AAF NICANS SLHDYAKIFP MNNATVAVDI YQGGVILGCL FGPAALYIWA IGLLAAGQSS TMTGTYAGQF VMEGFLRLRW SRFA RVLLT RSCAILPTVL VAVFRDLRDL SGLNDLLNVL QSLLLPFAVL PILTFTSMPT LMQEFANGLL NKVVTSSIMV LVCAI NLYF VVSYLPSLPH PAYFGLAALL AAAYLGLSTY LVWTCCLAHG ATFLAHSSHH HFLYGLLEED QKGETSGALE VLFQGP QGT EQKLISEEDL RGASMDEKTT GWRGGHVVEG LAGELEQLRA RLEHHPQGQR EP

UniProtKB: Natural resistance-associated macrophage protein 1

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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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 5 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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