+Open data
-Basic information
Entry | Database: PDB / ID: 7dde | ||||||||||||
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Title | Cryo-EM structure of the Ape4 and Nbr1 complex | ||||||||||||
Components | Aspartyl aminopeptidase 1,ZZ-type zinc finger-containing protein P35G2.11c,Maltose/maltodextrin-binding periplasmic protein | ||||||||||||
Keywords | HYDROLASE / aspartyl aminopeptidase / signaling protein / autophagy | ||||||||||||
Function / homology | Function and homology information NVT complex / aspartyl aminopeptidase / fungal-type vacuole lumen / cytoplasm to vacuole targeting by the NVT pathway / fungal-type vacuole / cargo receptor activity / detection of maltose stimulus / maltose transport complex / metalloaminopeptidase activity / carbohydrate transport ...NVT complex / aspartyl aminopeptidase / fungal-type vacuole lumen / cytoplasm to vacuole targeting by the NVT pathway / fungal-type vacuole / cargo receptor activity / detection of maltose stimulus / maltose transport complex / metalloaminopeptidase activity / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chaperone-mediated protein folding / multivesicular body / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / Golgi apparatus / proteolysis / zinc ion binding / membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.26 Å | ||||||||||||
Authors | Zhang, J. / Ye, K. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: EMBO J / Year: 2021 Title: Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1. Authors: Ying-Ying Wang / Jianxiu Zhang / Xiao-Man Liu / Yulu Li / Jianhua Sui / Meng-Qiu Dong / Keqiong Ye / Li-Lin Du / Abstract: In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast ...In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions. | ||||||||||||
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 | 7dde.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7dde.ent.gz | 935.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dde_validation.pdf.gz | 963.4 KB | Display | wwPDB validaton report |
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Full document | 7dde_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7dde_validation.xml.gz | 152.2 KB | Display | |
Data in CIF | 7dde_validation.cif.gz | 245.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/7dde ftp://data.pdbj.org/pub/pdb/validation_reports/dd/7dde | HTTPS FTP |
-Related structure data
Related structure data | 30652MC 7dd9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 102615.375 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: The fusion protein comprises of the full-length Ape4, a linker sequence (GFKKASSSDNKEQ), residues 53-129 of Nbr1, and maltose binding protein (MBP). Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast), (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: aap1, SPAC4F10.02, SPBP35G2.11c, malE, b4034, JW3994 / Production host: Schizosaccharomyces pombe 972h- (yeast) References: UniProt: O36014, UniProt: Q9P792, UniProt: P0AEX9, aspartyl aminopeptidase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: Ape4 and Nbr1 fusion protein / Type: COMPLEX Details: The fusion protein comprises of the full-length Ape4, a linker sequence (GFKKASSSDNKEQ), residues 53-129 of Nbr1, and maltose binding protein (MBP). Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.75 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Schizosaccharomyces pombe 972h- (yeast) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Homemade | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 5 seconds before plunging |
-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: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.4 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1799 |
EM imaging optics | Energyfilter name: GIF Tridiem 4K / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 32 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: T (tetrahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 414202 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.56 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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