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Yorodumi- EMDB-18126: Structural studies of human serum albumin using cryo-EM up to 0.3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18126 | |||||||||
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Title | Structural studies of human serum albumin using cryo-EM up to 0.38 nm resolution | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human serum albumin / monomer / 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: 3.77 Å | |||||||||
Authors | Slawek J / Taube M / Rawski M / Wojciechowska D / Kozak M | |||||||||
Funding support | Poland, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18126.map.gz | 31.1 MB | EMDB map data format | |
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Header (meta data) | emd-18126-v30.xml emd-18126.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_18126.png | 44.5 KB | ||
Others | emd_18126_half_map_1.map.gz emd_18126_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18126 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18126 | HTTPS FTP |
-Validation report
Summary document | emd_18126_validation.pdf.gz | 743.9 KB | Display | EMDB validaton report |
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Full document | emd_18126_full_validation.pdf.gz | 743.5 KB | Display | |
Data in XML | emd_18126_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_18126_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18126 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18126 | HTTPS FTP |
-Related structure data
Related structure data | 8q3fMC 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_18126.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18126_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18126_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Monomer of human serum albumin
Entire | Name: Monomer of human serum albumin |
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Components |
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-Supramolecule #1: Monomer of human serum albumin
Supramolecule | Name: Monomer of human serum albumin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 67 KDa |
-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 |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Details: PBS buffer at pH=7.4 (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4) |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 11116 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |