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- PDB-9f6p: Human NRAMP1 (SLC11A1) in complex with manganese, towards the inw... -

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Basic information

Entry
Database: PDB / ID: 9f6p
TitleHuman NRAMP1 (SLC11A1) in complex with manganese, towards the inward-open state
ComponentsNatural resistance-associated macrophage protein 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Feb 5, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natural resistance-associated macrophage protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1562
Polymers67,1011
Non-polymers551
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 1 / NRAMP 1 / Solute carrier family 11 member 1


Mass: 67100.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC11A1, LSH, NRAMP, NRAMP1 / Production host: Homo sapiens (human) / References: UniProt: P49279
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 NRAMP1 with manganese / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 60.8 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: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 5

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123180 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043814
ELECTRON MICROSCOPYf_angle_d0.9365202
ELECTRON MICROSCOPYf_dihedral_angle_d6.496526
ELECTRON MICROSCOPYf_chiral_restr0.048616
ELECTRON MICROSCOPYf_plane_restr0.005643

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