+Open data
-Basic information
Entry | Database: PDB / ID: 8r8t | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the inward-facing ethanolamine-bound FLVCR1 | ||||||
Components | Heme transporter FLVCR1 | ||||||
Keywords | MEMBRANE PROTEIN / MFS / ethanolamine transport / human transporter | ||||||
Function / homology | Function and homology information heme export / heme transport / heme transmembrane transporter activity / embryonic skeletal system morphogenesis / head morphogenesis / regulation of organ growth / Heme biosynthesis / heme biosynthetic process / embryonic digit morphogenesis / mitochondrial transport ...heme export / heme transport / heme transmembrane transporter activity / embryonic skeletal system morphogenesis / head morphogenesis / regulation of organ growth / Heme biosynthesis / heme biosynthetic process / embryonic digit morphogenesis / mitochondrial transport / blood vessel development / erythrocyte maturation / spleen development / erythrocyte differentiation / Iron uptake and transport / multicellular organism growth / mitochondrial inner membrane / in utero embryonic development / intracellular iron ion homeostasis / heme binding / mitochondrion / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Weng, T.-H. / Wu, D. / Safarian, S. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nature / Year: 2024 Title: Molecular mechanism of choline and ethanolamine transport in humans Authors: Weng, T.-H. / Wu, D. / Safarian, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8r8t.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8r8t.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 8r8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/8r8t ftp://data.pdbj.org/pub/pdb/validation_reports/r8/8r8t | HTTPS FTP |
---|
-Related structure data
Related structure data | 19009MC 8qcsC 8qctC 8qcxC 8qcyC 8qd0C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 60896.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLVCR1, FLVCR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y5Y0 |
---|---|
#2: Chemical | ChemComp-ETA / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ethanolamine-bound FLVCR1 monomer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.06 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2100 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5185344 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52147 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 8QCT Accession code: 8QCT / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
|