+Open data
-Basic information
Entry | Database: PDB / ID: 8f5b | ||||||
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Title | Human ABCA4 structure in complex with AMP-PNP | ||||||
Components | Retinal-specific phospholipid-transporting ATPase ABCA4 | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter / importer / membrane protein | ||||||
Function / homology | Function and homology information rod photoreceptor disc membrane / flippase activity / N-retinylidene-phosphatidylethanolamine flippase activity / all-trans retinal binding / phospholipid transfer to membrane / retinol transmembrane transporter activity / phospholipid transporter activity / 11-cis retinal binding / retinal metabolic process / ATPase-coupled intramembrane lipid transporter activity ...rod photoreceptor disc membrane / flippase activity / N-retinylidene-phosphatidylethanolamine flippase activity / all-trans retinal binding / phospholipid transfer to membrane / retinol transmembrane transporter activity / phospholipid transporter activity / 11-cis retinal binding / retinal metabolic process / ATPase-coupled intramembrane lipid transporter activity / phosphatidylethanolamine flippase activity / phototransduction, visible light / retinoid binding / photoreceptor cell maintenance / P-type phospholipid transporter / lipid transport / phospholipid translocation / retinoid metabolic process / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / photoreceptor outer segment / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / visual perception / ABC-family proteins mediated transport / transmembrane transport / photoreceptor disc membrane / cytoplasmic vesicle / intracellular membrane-bounded organelle / GTPase activity / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å | ||||||
Authors | Scortecci, J.F. / Van Petegem, F. / Molday, R.S. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Structural and Functional Characterization of ABCA4 in its Nucleotide-Bound State Authors: Scortecci, J.F. / Garces, F.A. / Molday, L.L. / Van Petegem, F. / Molday, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f5b.cif.gz | 359.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f5b.ent.gz | 268.2 KB | Display | PDB format |
PDBx/mmJSON format | 8f5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f5b_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8f5b_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8f5b_validation.xml.gz | 65 KB | Display | |
Data in CIF | 8f5b_validation.cif.gz | 94.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f5b ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f5b | HTTPS FTP |
-Related structure data
Related structure data | 28864MC 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: 256202.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCA4, ABCR / Production host: Homo sapiens (human) References: UniProt: P78363, P-type phospholipid transporter | ||||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | #5: Chemical | 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: ABCA4 structure in complex with AMP-PNP / Type: COMPLEX / Details: Recombinantly expressed human ABCA4 / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.25 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil 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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 825604 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149336 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 177.62 Å2 | ||||||||||||||||||||||||
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