8VG6 | pdb_00008vg6

Structure of Tulane virus

  • Classification: VIRUS
  • Organism(s): Tulane virus
  • Expression System: Platyrrhini
  • Mutation(s): No 

  • Deposited: 2023-12-22 Released: 2024-12-25 
  • Deposition Author(s): Yu, G., Li, K., Jiang, W.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8VG6

This is version 1.2 of the entry. See complete history

Literature

Antibody-Based Affinity Cryoelectron Microscopy at 2.6- angstrom Resolution.

Yu, G.Li, K.Huang, P.Jiang, X.Jiang, W.

(2016) Structure 24: 1984-1990

  • DOI: https://doi.org/10.1016/j.str.2016.09.008
  • Primary Citation Related Structures: 
    8VG6

  • PubMed Abstract: 

    The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging specimens such as those of low abundance and/or unpurified ones within reach of the cryo-EM technique. Despite the demonstrated successes for solving structures to low to intermediate resolutions, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ∼2.6-Å structure solved using the antibody-based affinity grid approach with low-concentration Tulane virus purified from a low-yield cell-culture system that has been challenging to standard cryo-EM grid preparation. Quantitative analyses of the structure indicate data and reconstruction quality comparable with the conventional grid preparation method using samples at high concentration.


  • Organizational Affiliation
    • Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA.

Macromolecule Content 

  • Total Structure Weight: 173.67 kDa 
  • Atom Count: 11,724 
  • Modeled Residue Count: 1,541 
  • Deposited Residue Count: 1,602 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C
534Tulane virusMutation(s): 0 
UniProt
Find proteins for B2Y6D0 (Tulane virus)
Explore B2Y6D0 
Go to UniProtKB:  B2Y6D0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2Y6D0
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI111095

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Data collection
  • Version 1.2: 2026-01-14
    Changes: Database references