+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37997 | |||||||||
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Title | Cryo-EM structure of human alpha-fetoprotein | |||||||||
Map data | ||||||||||
Sample |
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Keywords | N-glycosylation / Fatty acids / Metal ion / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information progesterone metabolic process / ovulation from ovarian follicle / small molecule binding / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular space / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.31 Å | |||||||||
Authors | Liu ZM / Li MS / Wu C / Liu K | |||||||||
Funding support | China, 1 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Structural characteristics of alpha-fetoprotein, including N-glycosylation, metal ion and fatty acid binding sites. Authors: Kun Liu / Cang Wu / Mingyue Zhu / Junnv Xu / Bo Lin / Haifeng Lin / Zhongmin Liu / Mengsen Li / Abstract: Alpha-fetoprotein (AFP), a serum glycoprotein, is expressed during embryonic development and the pathogenesis of liver cancer. It serves as a clinical tumor marker, function as a carcinogen, immune ...Alpha-fetoprotein (AFP), a serum glycoprotein, is expressed during embryonic development and the pathogenesis of liver cancer. It serves as a clinical tumor marker, function as a carcinogen, immune suppressor, and transport vehicle; but the detailed AFP structural information has not yet been reported. In this study, we used single-particle cryo-electron microscopy(cryo-EM) to analyze the structure of the recombinant AFP obtained a 3.31 Å cryo-EM structure and built an atomic model of AFP. We observed and identified certain structural features of AFP, including N-glycosylation at Asn251, four natural fatty acids bound to distinct domains, and the coordination of metal ions by residues His22, His264, His268, and Asp280. Furthermore, we compared the structural similarities and differences between AFP and human serum albumin. The elucidation of AFP's structural characteristics not only contributes to a deeper understanding of its functional mechanisms, but also provides a structural basis for developing AFP-based drug vehicles. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37997.map.gz | 25.4 MB | EMDB map data format | |
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Header (meta data) | emd-37997-v30.xml emd-37997.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37997_fsc.xml | 6.3 KB | Display | FSC data file |
Images | emd_37997.png | 55.2 KB | ||
Filedesc metadata | emd-37997.cif.gz | 5.7 KB | ||
Others | emd_37997_half_map_1.map.gz emd_37997_half_map_2.map.gz | 25 MB 25 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37997 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37997 | HTTPS FTP |
-Related structure data
Related structure data | 8x1nMC 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_37997.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37997_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37997_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of human alpha-fetoprotein
Entire | Name: Cryo-EM structure of human alpha-fetoprotein |
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Components |
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-Supramolecule #1: Cryo-EM structure of human alpha-fetoprotein
Supramolecule | Name: Cryo-EM structure of human alpha-fetoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Alpha-fetoprotein
Macromolecule | Name: Alpha-fetoprotein / 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: 68.757406 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKWVESIFLI FLLNFTESRT LHRNEYGIAS ILDSYQCTAE ISLADLATIF FAQFVQEATY KEVSKMVKDA LTAIEKPTGD EQSSGCLEN QLPAFLEELC HEKEILEKYG HSDCCSQSEE GRHNCFLAHK KPTPASIPLF QVPEPVTSCE AYEEDRETFM N KFIYEIAR ...String: MKWVESIFLI FLLNFTESRT LHRNEYGIAS ILDSYQCTAE ISLADLATIF FAQFVQEATY KEVSKMVKDA LTAIEKPTGD EQSSGCLEN QLPAFLEELC HEKEILEKYG HSDCCSQSEE GRHNCFLAHK KPTPASIPLF QVPEPVTSCE AYEEDRETFM N KFIYEIAR RHPFLYAPTI LLWAARYDKI IPSCCKAENA VECFQTKAAT VTKELRESSL LNQHACAVMK NFGTRTFQAI TV TKLSQKF TKVNFTEIQK LVLDVAHVHE HCCRGDVLDC LQDGEKIMSY ICSQQDTLSN KITECCKLTT LERGQCIIHA END EKPEGL SPNLNRFLGD RDFNQFSSGE KNIFLASFVH EYSRRHPQLA VSVILRVAKG YQELLEKCFQ TENPLECQDK GEEE LQKYI QESQALAKRS CGLFQKLGEY YLQNAFLVAY TKKAPQLTSS ELMAITRKMA ATAATCCQLS EDKLLACGEG AADII IGHL CIRHEMTPVN PGVGQCCTSS YANRRPCFSS LVVDETYVPP AFSDDKFIFH KDLCQAQGVA LQTMKQEFLI NLVKQK PQI TEEQLEAVIA DFSGLLEKCC QGQEQEVCFA EEGQKLISKT RAALGV UniProtKB: Alpha-fetoprotein |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 4 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |