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- EMDB-50235: Human divalent metal transporter 1 (DMT1/SLC11A2) in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-50235
TitleHuman divalent metal transporter 1 (DMT1/SLC11A2) in complex with manganese, in an occluded state
Map data
Sample
  • Complex: Complex of DMT1 with manganese ion
    • Protein or peptide: Natural resistance-associated macrophage protein 2
  • Ligand: MANGANESE (II) ION
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
Function / homology
Function and homology information


vanadium ion transmembrane transporter activity / vanadium ion transport / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / nickel cation transmembrane transporter activity / transition metal ion transmembrane transporter activity / solute:proton symporter activity / inorganic cation transmembrane transporter activity ...vanadium ion transmembrane transporter activity / vanadium ion transport / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / nickel cation transmembrane transporter activity / transition metal ion transmembrane transporter activity / solute:proton symporter activity / inorganic cation transmembrane transporter activity / cadmium ion transmembrane transport / Metal ion SLC transporters / manganese ion transport / nickel cation transport / detection of oxygen / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron import into cell / zinc ion transmembrane transporter activity / copper ion transmembrane transporter activity / retromer complex binding / iron ion transmembrane transporter activity / cobalt ion transport / cobalt ion transmembrane transporter activity / iron ion transmembrane transport / copper ion transport / basal part of cell / ferrous iron transmembrane transporter activity / vacuole / response to iron ion / dendrite morphogenesis / heme biosynthetic process / cadmium ion binding / erythrocyte development / brush border membrane / Iron uptake and transport / trans-Golgi network / : / recycling endosome / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / late endosome membrane / extracellular vesicle / apical part of cell / late endosome / iron ion transport / cellular response to oxidative stress / early endosome membrane / cytoplasmic vesicle / intracellular iron ion homeostasis / mitochondrial outer membrane / learning or memory / early endosome / lysosome / response to hypoxia / endosome membrane / apical plasma membrane / lysosomal membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / mitochondrion / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like
Similarity search - Domain/homology
Natural resistance-associated macrophage protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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_50235.png

Downloads & links

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Map

FileDownload / File: emd_50235.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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Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.99985635 - 1.5066994
Average (Standard dev.)0.0013777955 (±0.030481458)
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_50235_msk_1.map
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Half map: #2

Fileemd_50235_half_map_1.map
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Half map: #1

Fileemd_50235_half_map_2.map
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Sample components

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Entire : Complex of DMT1 with manganese ion

EntireName: Complex of DMT1 with manganese ion
Components
  • Complex: Complex of DMT1 with manganese ion
    • Protein or peptide: Natural resistance-associated macrophage protein 2
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Complex of DMT1 with manganese ion

SupramoleculeName: Complex of DMT1 with manganese ion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.6 kDa/nm

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Macromolecule #1: Natural resistance-associated macrophage protein 2

MacromoleculeName: Natural resistance-associated macrophage protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.93818 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSRKKQLKTE AAPHCELKSY SKNSATQVST MVLGPEQKMS DDSVSGDHGE SASLGNINPA YSNPSLSQSP GDSEEYFATY FNEKISIPE EEYSCFSFRK LWAFTGPGFL MSIAYLDPGN IESDLQSGAV AGFKLLWILL LATLVGLLLQ RLAARLGVVT G LHLAEVCH ...String:
MSRKKQLKTE AAPHCELKSY SKNSATQVST MVLGPEQKMS DDSVSGDHGE SASLGNINPA YSNPSLSQSP GDSEEYFATY FNEKISIPE EEYSCFSFRK LWAFTGPGFL MSIAYLDPGN IESDLQSGAV AGFKLLWILL LATLVGLLLQ RLAARLGVVT G LHLAEVCH RQYPKVPRVI LWLMVELAII GSDMQEVIGS AIAINLLSVG RIPLWGGVLI TIADTFVFLF LDKYGLRKLE AF FGFLITI MALTFGYEYV TVKPSQSQVL KGMFVPSCSG CRTPQIEQAV GIVGAVIMPH NMYLHSALVK SRQVNRNNKQ EVR EANKYF FIESCIALFV SFIINVFVVS VFAEAFFGKT NEQVVEVCTN TSSPHAGLFP KDNSTLAVDI YKGGVVLGCY FGPA ALYIW AVGILAAGQS STMTGTYSGQ FVMEGFLNLK WSRFARVVLT RSIAIIPTLL VAVFQDVEHL TGMNDFLNVL QSLQL PFAL IPILTFTSLR PVMSDFANGL GWRIAGGILV LIICSINMYF VVVYVRDLGH VALYVVAAVV SVAYLGFVFY LGWQCL IAL GMSFLDCGHT VSISKGLLTE EATRGYVKAL EVLFQGPQGT EQKLISEEDL RGASMDEKTT GWRGGHVVEG LAGELEQ LR ARLEHHPQGQ REP

UniProtKB: Natural resistance-associated macrophage protein 2

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Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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 / Material: GOLD / Mesh: 300 / 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: 1 / Average exposure time: 1.26 sec. / Average electron dose: 59.9 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170677
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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