+Open data
-Basic information
Entry | Database: PDB / ID: 6xg6 | |||||||||||||||||||||
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Title | Full-length human mitochondrial Hsp90 (TRAP1) with ADP-BeF3 | |||||||||||||||||||||
Components | Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion | |||||||||||||||||||||
Keywords | CHAPERONE / Hsp90 | |||||||||||||||||||||
Function / homology | Function and homology information translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / cell periphery / ATP-dependent protein folding chaperone ...translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) Streptococcus pyogenes (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Liu, Y.X. / Wang, F. / Agard, D.A. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Authors: Feng Wang / Yanxin Liu / Zanlin Yu / Sam Li / Shengjie Feng / Yifan Cheng / David A Agard / Abstract: Affinity grids have great potential to facilitate rapid preparation of even quite impure samples in single-particle cryo-electron microscopy (EM). Yet despite the promising advances of affinity grids ...Affinity grids have great potential to facilitate rapid preparation of even quite impure samples in single-particle cryo-electron microscopy (EM). Yet despite the promising advances of affinity grids over the past decades, no single strategy has demonstrated general utility. Here we chemically functionalize cryo-EM grids coated with mostly one or two layers of graphene oxide to facilitate affinity capture. The protein of interest is tagged using a system that rapidly forms a highly specific covalent bond to its cognate catcher linked to the grid via a polyethylene glycol (PEG) spacer. Importantly, the spacer keeps particles away from both the air-water interface and the graphene oxide surface, protecting them from potential denaturation and rendering them sufficiently flexible to avoid preferential sample orientation concerns. Furthermore, the PEG spacer successfully reduces nonspecific binding, enabling high-resolution reconstructions from a much cruder lysate sample. | |||||||||||||||||||||
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 | 6xg6.cif.gz | 241.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xg6.ent.gz | 184.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xg6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6xg6_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6xg6_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 6xg6_validation.cif.gz | 74.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/6xg6 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/6xg6 | HTTPS FTP |
-Related structure data
Related structure data | 22174MC 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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1 |
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-Components
#1: Protein | Mass: 87094.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Streptococcus pyogenes (bacteria) Gene: TRAP1, HSP75, fba2, E0F66_06355, GQY31_00620 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12931, UniProt: Q8G9G1 #2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | Has ligand of interest | N | |
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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: Trap1 dimer with ADP-BeF3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 0.147 MDa / Experimental value: YES | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid type: Quantifoil | ||||||||||||
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 |
Image recording | Electron dose: 69 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70998 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.1 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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