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- EMDB-37997: Cryo-EM structure of human alpha-fetoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-37997
TitleCryo-EM structure of human alpha-fetoprotein
Map data
Sample
  • Complex: Cryo-EM structure of human alpha-fetoprotein
    • Protein or peptide: Alpha-fetoprotein
  • Ligand: ZINC ION
  • Ligand: PALMITIC ACID
KeywordsN-glycosylation / Fatty acids / Metal ion / TRANSPORT PROTEIN
Function / homology
Function and homology information


progesterone metabolic process / ovulation from ovarian follicle / homeostasis of number of cells / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / immune response / endoplasmic reticulum lumen / apoptotic process / extracellular space / metal ion binding / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsLiu ZM / Li MS / Wu C / Liu K
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: 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
DepositionNov 8, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37997.png

Downloads & links

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Map

FileDownload / File: emd_37997.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 192 pix.
= 201.984 Å		1.05 Å/pix.
x 192 pix.
= 201.984 Å		1.05 Å/pix.
x 192 pix.
= 201.984 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.156
Minimum - Maximum-1.1392932 - 1.7850784
Average (Standard dev.)0.0003180747 (±0.04693345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 201.98401 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37997_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37997_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human alpha-fetoprotein

EntireName: Cryo-EM structure of human alpha-fetoprotein
Components
  • Complex: Cryo-EM structure of human alpha-fetoprotein
    • Protein or peptide: Alpha-fetoprotein
  • Ligand: ZINC ION
  • Ligand: PALMITIC ACID

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Supramolecule #1: Cryo-EM structure of human alpha-fetoprotein

SupramoleculeName: Cryo-EM structure of human alpha-fetoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Alpha-fetoprotein

MacromoleculeName: Alpha-fetoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.757406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144221
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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