+Open data
-Basic information
Entry | Database: PDB / ID: 9c5c | ||||||
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Title | Structure of Human Adaptor Protein Complex AP-3 in the Apo State | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Adaptor Protein complex / AP-3 / Lysosomal transport / Endosomal transport / Protein trafficking | ||||||
Function / homology | Function and homology information synaptic vesicle coating / synaptic vesicle budding from endosome / establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / zinc ion import into lysosome / AP-type membrane coat adaptor complex / skin epidermis development / synaptic vesicle membrane organization / AP-3 adaptor complex / anterograde synaptic vesicle transport ...synaptic vesicle coating / synaptic vesicle budding from endosome / establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / zinc ion import into lysosome / AP-type membrane coat adaptor complex / skin epidermis development / synaptic vesicle membrane organization / AP-3 adaptor complex / anterograde synaptic vesicle transport / microvesicle / endosome to melanosome transport / presynaptic endosome / Golgi to vacuole transport / synaptic vesicle recycling / postsynaptic recycling endosome / clathrin adaptor complex / platelet dense granule organization / melanosome assembly / granulocyte differentiation / postsynaptic neurotransmitter receptor internalization / positive regulation of NK T cell differentiation / GTP-dependent protein binding / neurotransmitter receptor transport, postsynaptic endosome to lysosome / clathrin-coated vesicle membrane / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / protein targeting to vacuole / protein targeting to lysosome / respiratory system process / melanosome organization / anterograde axonal transport / protein localization to membrane / intracellular zinc ion homeostasis / protein localization to cell surface / toll-like receptor signaling pathway / Golgi Associated Vesicle Biogenesis / lysosome organization / lung morphogenesis / Association of TriC/CCT with target proteins during biosynthesis / homeostasis of number of cells / intracellular transport / single fertilization / hematopoietic progenitor cell differentiation / vesicle-mediated transport / transport vesicle / axon cytoplasm / intracellular protein transport / mRNA transcription by RNA polymerase II / cytoplasmic vesicle membrane / protein modification process / terminal bouton / cell morphogenesis / small GTPase binding / endocytosis / blood coagulation / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / synaptic vesicle / protein phosphatase binding / cytoplasmic vesicle / spermatogenesis / early endosome / lysosome / postsynapse / endosome membrane / inflammatory response / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Model details | MODEL GENERATED BY ROSETTA VERSION 2020.08+release.cb1caba | ||||||
Authors | Begley, M.C. / Baker, R.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: A structure-based mechanism for initiation of AP-3 coated vesicle formation Authors: Begley, M. / Baker, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c5c.cif.gz | 259.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c5c.ent.gz | 205 KB | Display | PDB format |
PDBx/mmJSON format | 9c5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c5c_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 9c5c_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9c5c_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 9c5c_validation.cif.gz | 87.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/9c5c ftp://data.pdbj.org/pub/pdb/validation_reports/c5/9c5c | HTTPS FTP |
-Related structure data
Related structure data | 45214MC 9c58C 9c59C 9c5aC 9c5bC C: citing same article (ref.) M: map data used to model this data |
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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: 66164.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP3D1, PRO0039 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: O14617 |
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#2: Protein | Mass: 65602.797 Da / Num. of mol.: 1 / Mutation: residues 261-293 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP3B1, ADTB3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: O00203 |
#3: Protein | Mass: 14274.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP3M1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: Q9Y2T2 |
#4: Protein | Mass: 17412.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP3S1, CLAPS3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: Q92572 |
Has protein modification | N |
-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: Human Adaptor Protein Complex AP-3 in the Apo state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.215 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 Star | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: 1x PBS (pH 7.4), 300mM NaCl, 1mM TCEP | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Specimen appeared as a monodisperse peak via size exclusion chromatography (SEC) | ||||||||||||||||||||||||||||||
Specimen support | Details: Used Quantifoil Active grids- Backside gold coated before plasma cleaned. 12 mA used for plasma cleaning Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: SPOTITON / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 296 K / Details: Commercialized version - Chameleon |
-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 magnification: 105000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49.97 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) Details: 4 datasets collected, processed independently, and merged. |
EM imaging optics | Energyfilter name: TFS Selectris / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Details: Mixture of blob picker, template picker, crYOLO, and Topaz | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1205158 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |