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Yorodumi- PDB-8q3f: Structural studies of human serum albumin using cryo-EM up to 0.3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q3f | ||||||
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Title | Structural studies of human serum albumin using cryo-EM up to 0.38 nm resolution | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / human serum albumin / monomer | ||||||
Function / homology | Function and homology information exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / pyridoxal phosphate binding / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.77 Å | ||||||
Authors | Slawek, J. / Taube, M. / Rawski, M. / Wojciechowska, D. / Kozak, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Structural studies of human serum albumin using cryo-EM up to 0.38 nm resolution Authors: Slawek, J. / Taube, M. / Rawski, M. / Wojciechowska, D. / Kozak, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q3f.cif.gz | 132.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q3f.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 8q3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q3f_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8q3f_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8q3f_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 8q3f_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/8q3f ftp://data.pdbj.org/pub/pdb/validation_reports/q3/8q3f | HTTPS FTP |
-Related structure data
Related structure data | 18126MC 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: 66571.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768 |
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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: Monomer of human serum albumin / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.067 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 Details: PBS buffer at pH=7.4 (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4) |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS 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: 1500 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 11116 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1663068 Details: from template picker with templates generated from 49615 particles picked by blob picker on 200 micrographs | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185569 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4G03 Pdb chain-ID: B / Accession code: 4G03 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 180.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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