+Open data
-Basic information
Entry | Database: PDB / ID: 8qcz | ||||||
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Title | Cryo-EM structure of the outward-facing heme-bound FLVCR2 | ||||||
Components | Heme transporter FLVCR2 | ||||||
Keywords | MEMBRANE PROTEIN / MFS / choline transport / human transporter | ||||||
Function / homology | Function and homology information heme export / heme transmembrane transporter activity / mitochondrial membrane / heme binding / endoplasmic reticulum membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Weng, T.-H. / Wu, D. / Safarian, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the outward-facing heme-bound FLVCR2 Authors: Weng, T.-H. / Wu, D. / Safarian, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qcz.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qcz.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 8qcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qcz_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8qcz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8qcz_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 8qcz_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/8qcz ftp://data.pdbj.org/pub/pdb/validation_reports/qc/8qcz | HTTPS FTP |
-Related structure data
Related structure data | 18338MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 58277.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLVCR2, C14orf58 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9UPI3 |
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#2: Chemical | ChemComp-HEM / |
Has ligand of interest | Y |
-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: FLVCR monomer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.058 MDa / Experimental value: YES |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5419952 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51266 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Accession code: AF-Q9UPI3-F1 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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