8GVK | pdb_00008gvk

Cryo-EM structure of streptavidin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8GVK

This is version 1.3 of the entry. See complete history

Literature

Uniform thin ice on ultraflat graphene for high-resolution cryo-EM.

Zheng, L.Liu, N.Gao, X.Zhu, W.Liu, K.Wu, C.Yan, R.Zhang, J.Gao, X.Yao, Y.Deng, B.Xu, J.Lu, Y.Liu, Z.Li, M.Wei, X.Wang, H.W.Peng, H.

(2023) Nat Methods 20: 123-130

  • DOI: https://doi.org/10.1038/s41592-022-01693-y
  • Primary Citation Related Structures: 
    7XGY, 7YIM, 8GVK

  • PubMed 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, 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.


  • Organizational Affiliation
    • Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 75.4 kDa 
  • Atom Count: 3,567 
  • Modeled Residue Count: 476 
  • Deposited Residue Count: 732 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Streptavidin
A, B, C, D
183StreptomycesMutation(s): 0 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China52021006

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-01-25
    Changes: Database references
  • Version 1.3: 2024-07-03
    Changes: Data collection