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- EMDB-33861: Cryo-EM structure of human Alpha-fetoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-33861
TitleCryo-EM structure of human Alpha-fetoprotein
Map data
Sample
  • Complex: Alpha-fetoprotein with no symmetry
    • Protein or peptide: Alpha-fetoprotein
Keywordsmetal binding / fatty acids binding / METAL BINDING 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
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: 2.6 Å
AuthorsLiu N / Liu K / Wu C / Liu Z / Li M / Wang J / Wang HW
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Methods / Year: 2023
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
DepositionJul 17, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33861.png

Downloads & links

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Map

FileDownload / File: emd_33861.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 150 pix.
= 155.73 Å		1.04 Å/pix.
x 150 pix.
= 155.73 Å		1.04 Å/pix.
x 150 pix.
= 155.73 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0382 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.41
Minimum - Maximum-2.4771485 - 3.9402535
Average (Standard dev.)-0.005645023 (±0.09546304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 155.73 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33861_msk_1.map
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Half map: #1

Fileemd_33861_half_map_1.map
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Half map: #2

Fileemd_33861_half_map_2.map
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Sample components

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Entire : Alpha-fetoprotein with no symmetry

EntireName: Alpha-fetoprotein with no symmetry
Components
  • Complex: Alpha-fetoprotein with no symmetry
    • Protein or peptide: Alpha-fetoprotein

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Supramolecule #1: Alpha-fetoprotein with no symmetry

SupramoleculeName: Alpha-fetoprotein with no symmetry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67 KDa

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE

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Electron microscopy

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

5hoz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 354264
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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