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Yorodumi- EMDB-43089: Cryogenic electron microscopy structure of human serum albumin in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43089 | |||||||||
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Title | Cryogenic electron microscopy structure of human serum albumin in complex with salicylic acid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Human Serum Albumin / Salicylic acid / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / 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) / pyridoxal phosphate binding / Platelet degranulation / 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 | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Catalano C / Lucier KW / To D / Senko S / Tran NL / Farwell AC / Silva SM / Dip PV / Poweleit N / Scapin G | |||||||||
Funding support | 1 items
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Citation | Journal: J Struct Biol / Year: 2024 Title: The CryoEM structure of human serum albumin in complex with ligands. Authors: Claudio Catalano / Kyle W Lucier / Dennis To / Skerdi Senko / Nhi L Tran / Ashlyn C Farwell / Sabrina M Silva / Phat V Dip / Nicole Poweleit / Giovanna Scapin / Abstract: Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60 % of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a ...Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60 % of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a facilitator in the distribution of endobiotics and xenobiotics within the organism. In this paper we report the cryoEM structures of HSA in the apo form and in complex with two ligands (salicylic acid and teniposide) at a resolution of 3.5, 3.7 and 3.4 Å, respectively. We expand upon previously published work and further demonstrate that sub-4 Å maps of ∼60 kDa proteins can be routinely obtained using a 200 kV microscope, employing standard workflows. Most importantly, these maps allowed for the identification of small molecule ligands, emphasizing the practical applicability of this methodology and providing a starting point for subsequent computational modeling and in silico optimization. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43089.map.gz | 306.6 MB | EMDB map data format | |
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Header (meta data) | emd-43089-v30.xml emd-43089.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43089_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_43089.png | 55.6 KB | ||
Masks | emd_43089_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-43089.cif.gz | 6 KB | ||
Others | emd_43089_half_map_1.map.gz emd_43089_half_map_2.map.gz | 301.1 MB 301.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43089 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43089 | HTTPS FTP |
-Validation report
Summary document | emd_43089_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_43089_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_43089_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | emd_43089_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43089 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43089 | HTTPS FTP |
-Related structure data
Related structure data | 8vaeMC 8vacC 8vafC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43089.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.566 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43089_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43089_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43089_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : human serum albumin in complex with salicyl acid
Entire | Name: human serum albumin in complex with salicyl acid |
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Components |
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-Supramolecule #1: human serum albumin in complex with salicyl acid
Supramolecule | Name: human serum albumin in complex with salicyl acid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Serum albumin
Macromolecule | Name: Serum albumin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 66.571219 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DAHKSEVAHR FKDLGEENFK ALVLIAFAQY LQQCPFEDHV KLVNEVTEFA KTCVADESAE NCDKSLHTLF GDKLCTVATL RETYGEMAD CCAKQEPERN ECFLQHKDDN PNLPRLVRPE VDVMCTAFHD NEETFLKKYL YEIARRHPYF YAPELLFFAK R YKAAFTEC ...String: DAHKSEVAHR FKDLGEENFK ALVLIAFAQY LQQCPFEDHV KLVNEVTEFA KTCVADESAE NCDKSLHTLF GDKLCTVATL RETYGEMAD CCAKQEPERN ECFLQHKDDN PNLPRLVRPE VDVMCTAFHD NEETFLKKYL YEIARRHPYF YAPELLFFAK R YKAAFTEC CQAADKAACL LPKLDELRDE GKASSAKQRL KCASLQKFGE RAFKAWAVAR LSQRFPKAEF AEVSKLVTDL TK VHTECCH GDLLECADDR ADLAKYICEN QDSISSKLKE CCEKPLLEKS HCIAEVENDE MPADLPSLAA DFVESKDVCK NYA EAKDVF LGMFLYEYAR RHPDYSVVLL LRLAKTYETT LEKCCAAADP HECYAKVFDE FKPLVEEPQN LIKQNCELFE QLGE YKFQN ALLVRYTKKV PQVSTPTLVE VSRNLGKVGS KCCKHPEAKR MPCAEDYLSV VLNQLCVLHE KTPVSDRVTK CCTES LVNR RPCFSALEVD ETYVPKEFNA ETFTFHADIC TLSEKERQIK KQTALVELVK HKPKATKEQL KAVMDDFAAF VEKCCK ADD KETCFAEEGK KLVAASQAAL GL UniProtKB: Albumin |
-Macromolecule #2: 2-HYDROXYBENZOIC ACID
Macromolecule | Name: 2-HYDROXYBENZOIC ACID / type: ligand / ID: 2 / Number of copies: 3 / Formula: SAL |
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Molecular weight | Theoretical: 138.121 Da |
Chemical component information | ChemComp-SAL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Name: PBS |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9616 / Average exposure time: 3.7 sec. / Average electron dose: 36.43 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 240000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |