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CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.

Perilla, J.R.Zhao, G.Lu, M.Ning, J.Hou, G.Byeon, I.L.Gronenborn, A.M.Polenova, T.Zhang, P.

(2017) J Phys Chem B 121: 3853-3863

  • DOI: 10.1021/acs.jpcb.6b13105

  • PubMed Abstract: 
  • Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4 ...

    Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 Å, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging. Here, we present a novel integrated strategy to combine the highly complementary experimental data from cryoEM and NMR computationally by molecular dynamics simulations to derive an atomistic model, which is not attainable by either approach alone. We use the HIV-1 capsid protein (CA) C-terminal domain as well as the large capsid assembly to demonstrate the feasibility of this approach, termed NMR CS-biased cryoEM structure refinement.


    Organizational Affiliation

    Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag polyprotein
A, B, C, D, E, F
221Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12493
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-04 
  • Released Date: 2017-03-01 
  • Deposition Author(s): Perilla, J.R.

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesP50 GM082251
National Institutes of HealthUnited StatesP41 GM104601
National Institutes of HealthUnited StatesR01 GM067887
NSFUnited StatesOCI-0725070
NSFUnited StatesACI-1238993
NSFUnited StatesACI-1440026

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Data collection
  • Version 1.3: 2017-12-06
    Type: Structure summary