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- EMDB-34978: Cryo-EM structure of streptavidin -

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Basic information

Entry
Database: EMDB / ID: EMD-34978
TitleCryo-EM structure of streptavidin
Map data
Sample
  • Complex: streptavidin
    • Protein or peptide: Streptavidin
  • Ligand: water
KeywordsComplex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsXu J / Liu N / Wang HW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Self-assembled superstructure alleviates air-water interface effect in cryo-EM.
Authors: Liming Zheng / Jie Xu / Weihua Wang / Xiaoyin Gao / Chao Zhao / Weijun Guo / Luzhao Sun / Hang Cheng / Fanhao Meng / Buhang Chen / Weiyu Sun / Xia Jia / Xiong Zhou / Kai Wu / Zhongfan Liu / ...Authors: Liming Zheng / Jie Xu / Weihua Wang / Xiaoyin Gao / Chao Zhao / Weijun Guo / Luzhao Sun / Hang Cheng / Fanhao Meng / Buhang Chen / Weiyu Sun / Xia Jia / Xiong Zhou / Kai Wu / Zhongfan Liu / Feng Ding / Nan Liu / Hong-Wei Wang / Hailin Peng /
Abstract: Cryo-electron microscopy (cryo-EM) has been widely used to reveal the structures of proteins at atomic resolution. One key challenge is that almost all proteins are predominantly adsorbed to the air- ...Cryo-electron microscopy (cryo-EM) has been widely used to reveal the structures of proteins at atomic resolution. One key challenge is that almost all proteins are predominantly adsorbed to the air-water interface during standard cryo-EM specimen preparation. The interaction of proteins with air-water interface will significantly impede the success of reconstruction and achievable resolution. Here, we highlight the critical role of impenetrable surfactant monolayers in passivating the air-water interface problems, and develop a robust effective method for high-resolution cryo-EM analysis, by using the superstructure GSAMs which comprises surfactant self-assembled monolayers (SAMs) and graphene membrane. The GSAMs works well in enriching the orientations and improving particle utilization ratio of multiple proteins, facilitating the 3.3-Å resolution reconstruction of a 100-kDa protein complex (ACE2-RBD), which shows strong preferential orientation using traditional specimen preparation protocol. Additionally, we demonstrate that GSAMs enables the successful determinations of small proteins (<100 kDa) at near-atomic resolution. This study expands the understanding of SAMs and provides a key to better control the interaction of protein with air-water interface.
History
DepositionDec 15, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34978.png

Downloads & links

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Map

FileDownload / File: emd_34978.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 200 pix.
= 103.82 Å		0.52 Å/pix.
x 200 pix.
= 103.82 Å		0.52 Å/pix.
x 200 pix.
= 103.82 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5191 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.8795018 - 1.1183499
Average (Standard dev.)0.009267804 (±0.06428383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 103.82 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34978_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_34978_half_map_2.map
Projections & Slices
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Sample components

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Entire : streptavidin

EntireName: streptavidin
Components
  • Complex: streptavidin
    • Protein or peptide: Streptavidin
  • Ligand: water

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Supramolecule #1: streptavidin

SupramoleculeName: streptavidin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: on graphene/SAMs membranes
Source (natural)Organism: Streptomyces avidinii (bacteria)

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Macromolecule #1: Streptavidin

MacromoleculeName: Streptavidin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces avidinii (bacteria)
Molecular weightTheoretical: 12.596641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GITGTWYNQL GSTFIVTAGA DGALTGTYES AVGNAESRYV LTGRYDSAPA TDGSGTALGW TVAWKNNYRN AHSATTWSGQ YVGGAEARI NTQWLLTSGT TEANAWKSTL VGHDTFTKVK

UniProtKB: Streptavidin

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 19 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.8
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99871
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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