+Open data
-Basic information
Entry | Database: PDB / ID: 7vqo | ||||||||||||
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Title | Cryo-EM structure of Ams1 bound to the FW domain of Nbr1 | ||||||||||||
Components | Ams1, Nbr1 and malE fusion protein | ||||||||||||
Keywords | HYDROLASE / glycoside hydrolase / signaling protein / autophagy | ||||||||||||
Function / homology | Function and homology information alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...alpha-mannosidase / alpha-mannosidase activity / mannose metabolic process / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / periplasmic space / DNA damage response / zinc ion binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Chaetomium thermophilum DSM 1495 (fungus) Escherichia coli K-12 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å | ||||||||||||
Authors | Zhang, J. / Ye, K. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1 Authors: Zhang, J. / Wang, Y.Y. / Pan, Z.Q. / Li, Y. / Sui, J. / Du, L.L. / Ye, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vqo.cif.gz | 870.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vqo.ent.gz | 691.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vqo ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vqo | HTTPS FTP |
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-Related structure data
Related structure data | 32091MC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper:
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-Components
#1: Protein | Mass: 181676.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP).,The fusion protein ...Details: The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP).,The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP). Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus), (gene. exp.) Chaetomium thermophilum DSM 1495 (fungus), (gene. exp.) Escherichia coli K-12 (bacteria) Strain: DSM 1495, K-12 / Gene: CTHT_0067100, CTHT_0062850, malE / Production host: Schizosaccharomyces pombe 972h- (yeast) References: UniProt: G0SGP6, UniProt: G0SE85, UniProt: P0AEX9, alpha-mannosidase #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: Ams1, Nbr1 and malE fusion protein / Type: COMPLEX Details: The fusion protein comprises of the full-length Ams1, a linker sequence (GGGGSGGGFKKASSSDNKEQGGGGSGGGSG), residues 635-775 of Nbr1, and maltose binding protein (MBP). Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.52 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: NICKEL/TITANIUM / Grid type: Homemade | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 3 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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2925 |
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 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 692409 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6LZ1 | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.21 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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