← Back to search
9f6n

Human divalent metal transporter 1 (DMT1/SLC11A2) in complex with manganese, in an occluded state

Method: ELECTRON MICROSCOPY Dmax: 75.3 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Natural resistance-associated macrophage protein 2

Homo sapiens

UniProt P49281

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–590 Not recorded MN MANGANESE (II) ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9F6N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 545–568（24 aa） Fragment：UNP residues 545-568
Not recorded SO4 SULFATE ION × 10 GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.75 M AmSO4, 0.1 M MES pH 6.0, 15% Glycerol
Resolution 3.20 Å R-free 0.259
5F0M Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled) Deposited 2015-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 549–560（12 aa） Fragment：UNP residues 549-560
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol
Resolution 3.10 Å R-free 0.254
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 549–560（12 aa）
Mutation：L557M Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 20 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol
Resolution 2.78 Å R-free 0.261
9F6O Human divalent metal transporter 1 (DMT1/SLC11A2) in complex with sybody 1, in an occluded state Deposited 2024-05-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–590（589 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRAM2_HUMAN
Isoform P49281-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–591； UniProt 2–590

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9f6n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9f6n
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9f6n
Deposition date deposition_date2024-05-02
Structure title titleHuman divalent metal transporter 1 (DMT1/SLC11A2) in complex with manganese, in an occluded state
Keywords keywords;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, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.57 Å
Radius of gyration Rg (electron density) rg_electron22.47 Å
Forward intensity I(0) i037448200.00
Molecular weight molecular_weight51787.0 kDa
Excluded volume excluded_volume66811 ų
Envelope volume envelope_volume78650 ų
Hydration-shell volume shell_volume28383 ų
Envelope diameter envelope_diameter76.1 Å
Shell Rg shell_rg30.28 Å
Envelope Rg envelope_rg22.79 Å
Shape Rg shape_rg22.47 Å
Total Rg total_rg23.47 Å
Total atoms total_atoms3652
Residues n_residues471
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax75.3 Å
Rg (real space) rg_real23.49 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real3.7450e+07
I(0) uncertainty (real space) i0_real_error4.5790e+05
Rg (reciprocal space) rg_reciprocal23.51 Å
I(0) (reciprocal space) i0_reciprocal37450000.0000
Solution quality estimate total_estimate0.8967
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.2 Å
Skewness Skewness skewness0.276
Kurtosis Kurtosis kurtosis-0.327
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7280000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.988
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)