+Open data
-Basic information
Entry | Database: PDB / ID: 6hd1 | ||||||||||||
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Title | human STEAP4 bound to NADPH, FAD and heme. | ||||||||||||
Components | Metalloreductase STEAP4 | ||||||||||||
Keywords | MEMBRANE PROTEIN / Enzyme / Metalloreductase / Electron Transfer / Cofactor-binding | ||||||||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / ferric-chelate reductase (NADPH) activity / cupric reductase (NADH) activity / iron import into cell / copper ion import / Transferrin endocytosis and recycling / fat cell differentiation / protein homotrimerization / FAD binding / early endosome membrane ...Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / ferric-chelate reductase (NADPH) activity / cupric reductase (NADH) activity / iron import into cell / copper ion import / Transferrin endocytosis and recycling / fat cell differentiation / protein homotrimerization / FAD binding / early endosome membrane / electron transfer activity / endosome membrane / endosome / Golgi membrane / heme binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Oosterheert, W. / van Bezouwen, L.S. / Rodenburg, R.N.P. / Forster, F. / Mattevi, A. / Gros, P. | ||||||||||||
Funding support | Netherlands, Italy, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Cryo-EM structures of human STEAP4 reveal mechanism of iron(III) reduction. Authors: Wout Oosterheert / Laura S van Bezouwen / Remco N P Rodenburg / Joke Granneman / Friedrich Förster / Andrea Mattevi / Piet Gros / Abstract: Enzymes of the six-transmembrane epithelial antigen of the prostate (STEAP) family reduce Fe and Cu ions to facilitate metal-ion uptake by mammalian cells. STEAPs are highly upregulated in several ...Enzymes of the six-transmembrane epithelial antigen of the prostate (STEAP) family reduce Fe and Cu ions to facilitate metal-ion uptake by mammalian cells. STEAPs are highly upregulated in several types of cancer, making them potential therapeutic targets. However, the structural basis for STEAP-catalyzed electron transfer through an array of cofactors to metals at the membrane luminal side remains elusive. Here, we report cryo-electron microscopy structures of human STEAP4 in absence and presence of Fe-NTA. Domain-swapped, trimeric STEAP4 orients NADPH bound to a cytosolic domain onto axially aligned flavin-adenine dinucleotide (FAD) and a single b-type heme that cross the transmembrane-domain to enable electron transfer. Substrate binding within a positively charged ring indicates that iron gets reduced while in complex with its chelator. These molecular principles of iron reduction provide a basis for exploring STEAPs as therapeutic targets. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6hd1.cif.gz | 249.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hd1.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hd1_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6hd1_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6hd1_validation.xml.gz | 54.4 KB | Display | |
Data in CIF | 6hd1_validation.cif.gz | 76.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/6hd1 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/6hd1 | HTTPS FTP |
-Related structure data
Related structure data | 0200MC 0199C 6hcyC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein / Sugars , 2 types, 6 molecules CAB
#1: Protein | Mass: 52036.000 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STEAP4, STAMP2, TNFAIP9 / Plasmid: pUPE / Details (production host): pUPE 3423 / Cell (production host): HEK293 GNTI- / Cell line (production host): HEK293 GNTI- / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY References: UniProt: Q687X5, Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor #5: Sugar | |
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-Non-polymers , 4 types, 12 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: homotrimer of human STEAP4. / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.152 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 GNTI- / Plasmid: pUPE 3423 | ||||||||||||||||||||
Buffer solution | pH: 5.5 / Details: 25 mM MES pH 5.5 200 mM NaCl 0.08% digitonin (w/v) | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: human STEAP4 was purified from the HEK293 GNTI- cell membrane through Strep-affinity chromatography and size-exclusion chromatography (SEC). After SEC in digitonin, the sample was ...Details: human STEAP4 was purified from the HEK293 GNTI- cell membrane through Strep-affinity chromatography and size-exclusion chromatography (SEC). After SEC in digitonin, the sample was monodisperse. Cofactors NADPH and FAD were added before grid freezing. | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: blot time 4seconds blot force 0 |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA Details: 200 kV Talos Arctica at Utrecht University, the Netherlands. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 6 sec. / Electron dose: 45.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2321 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 24 / Used frames/image: 1-24 |
-Processing
Software |
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EM software |
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CTF correction | Details: performed in GCTF. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 421438 / Details: Autopicked in Relion. | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209075 / Details: performed by RELION. / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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