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- PDB-9f6o: Human divalent metal transporter 1 (DMT1/SLC11A2) in complex with... -

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Basic information

Entry
Database: PDB / ID: 9f6o
TitleHuman divalent metal transporter 1 (DMT1/SLC11A2) in complex with sybody 1, in an occluded state
Components
  • Natural resistance-associated macrophage protein 2
  • Sybody 1
KeywordsTRANSPORT PROTEIN / Iron transport / Manganese transport / Transition metal transport / Divalent metal transport / Metal transport / Transporter / Membrane protein / SLC / Iron uptake / Iron homeostasis / LeuT fold / Small membrane 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 / copper ion transmembrane transporter activity / cobalt ion transport / cobalt ion transmembrane transporter activity / retromer complex binding / ferrous iron transmembrane transporter activity / iron ion transmembrane transporter activity / zinc ion transmembrane transporter activity / iron ion transmembrane transport / copper ion transport / basal part of cell / vacuole / response to iron ion / heme biosynthetic process / dendrite morphogenesis / cadmium ion binding / erythrocyte development / trans-Golgi network / Iron uptake and transport / brush border membrane / recycling endosome / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / late endosome membrane / apical part of cell / late endosome / extracellular vesicle / iron ion transport / cellular response to oxidative stress / early endosome membrane / cytoplasmic vesicle / mitochondrial outer membrane / intracellular iron ion homeostasis / learning or memory / early endosome / response to hypoxia / lysosome / endosome membrane / apical plasma membrane / lysosomal membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / mitochondrion / nucleus / membrane / 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)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLiziczai, M. / Dutzler, R.
Funding support Switzerland, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 2.0Jan 22, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_imaging / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_validate_torsion / refine / refine_ls_restr / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_admin.last_update / _em_imaging.microscope_model ..._em_admin.last_update / _em_imaging.microscope_model / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _refine.ls_d_res_high / _refine.pdbx_stereochemistry_target_values / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_conn.pdbx_dist_value / _struct_sheet.number_strands
Description: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 2.2Feb 5, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Natural resistance-associated macrophage protein 2
B: Sybody 1


Theoretical massNumber of molelcules
Total (without water)88,3522
Polymers88,3522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Natural resistance-associated macrophage protein 2


Mass: 71938.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC11A2 / Production host: Homo sapiens (human) / References: UniProt: P49281
#2: Antibody Sybody 1


Mass: 16414.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of DMT1 and Sybody 1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 80.7 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T / Plasmid: pcDXC3MS
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 61.76 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72182 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034717
ELECTRON MICROSCOPYf_angle_d0.5476418
ELECTRON MICROSCOPYf_dihedral_angle_d3.894637
ELECTRON MICROSCOPYf_chiral_restr0.036738
ELECTRON MICROSCOPYf_plane_restr0.003797

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