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Open data
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Basic information
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Title | Cryo-EM structure of human Alpha-fetoprotein | |||||||||
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![]() | metal binding / fatty acids binding / METAL BINDING PROTEIN | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
![]() | Liu N / Liu K / Wu C / Liu Z / Li M / Wang J / Wang HW | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Uniform thin ice on ultraflat graphene for high-resolution cryo-EM. Authors: Liming Zheng / Nan Liu / Xiaoyin Gao / Wenqing Zhu / Kun Liu / Cang Wu / Rui Yan / Jincan Zhang / Xin Gao / Yating Yao / Bing Deng / Jie Xu / Ye Lu / Zhongmin Liu / Mengsen Li / Xiaoding Wei ...Authors: Liming Zheng / Nan Liu / Xiaoyin Gao / Wenqing Zhu / Kun Liu / Cang Wu / Rui Yan / Jincan Zhang / Xin Gao / Yating Yao / Bing Deng / Jie Xu / Ye Lu / Zhongmin Liu / Mengsen Li / Xiaoding Wei / Hong-Wei Wang / Hailin Peng / ![]() Abstract: Cryo-electron microscopy (cryo-EM) visualizes the atomic structure of macromolecules that are embedded in vitrified thin ice at their close-to-native state. However, the homogeneity of ice thickness, ...Cryo-electron microscopy (cryo-EM) visualizes the atomic structure of macromolecules that are embedded in vitrified thin ice at their close-to-native state. However, the homogeneity of ice thickness, a key factor to ensure high image quality, is poorly controlled during specimen preparation and has become one of the main challenges for high-resolution cryo-EM. Here we found that the uniformity of thin ice relies on the surface flatness of the supporting film, and developed a method to use ultraflat graphene (UFG) as the support for cryo-EM specimen preparation to achieve better control of vitreous ice thickness. We show that the uniform thin ice on UFG improves the image quality of vitrified specimens. Using such a method we successfully determined the three-dimensional structures of hemoglobin (64 kDa), α-fetoprotein (67 kDa) with no symmetry, and streptavidin (52 kDa) at a resolution of 3.5 Å, 2.6 Å and 2.2 Å, respectively. Furthermore, our results demonstrate the potential of UFG for the fields of cryo-electron tomography and structure-based drug discovery. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.7 KB 14.7 KB | Display Display | ![]() |
Images | ![]() | 80.8 KB | ||
Masks | ![]() | 12.9 MB | ![]() | |
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 11.9 MB 11.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 759.4 KB | Display | ![]() |
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Full document | ![]() | 758.9 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yimMC ![]() 7xgyC ![]() 8gvkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0382 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
File | emd_33861_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33861_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Alpha-fetoprotein with no symmetry
Entire | Name: Alpha-fetoprotein with no symmetry |
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Components |
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-Supramolecule #1: Alpha-fetoprotein with no symmetry
Supramolecule | Name: Alpha-fetoprotein with no symmetry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 67 KDa |
-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: ![]() |
Molecular weight | Theoretical: 68.757406 KDa |
Recombinant expression | Organism: ![]() |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 354264 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |