5OB4

NMR spatial structure of HER2 TM domain dimer in DPC micelles.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins.

Lesovoy, D.M.Mineev, K.S.Bragin, P.E.Bocharova, O.V.Bocharov, E.V.Arseniev, A.S.

(2017) J. Biomol. NMR 69: 165-179

  • DOI: 10.1007/s10858-017-0146-1

  • PubMed Abstract: 
  • In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the ...

    In the case of soluble proteins, chemical shift mapping is used to identify the intermolecular interfaces when the NOE-based calculations of spatial structure of the molecular assembly are impossible or impracticable. However, the reliability of the membrane protein interface mapping based on chemical shifts or other relevant parameters was never assessed. In the present work, we investigate the predictive power of various NMR parameters that can be used for mapping of helix-helix interfaces in dimeric TM domains. These parameters are studied on a dataset containing three structures of helical dimers obtained for two different proteins in various membrane mimetics. We conclude that the amide chemical shifts have very little predictive value, while the methyl chemical shifts could be used to predict interfaces, though with great care. We suggest an approach based on conversion of the carbon NMR relaxation parameters of methyl groups into parameters of motion, and one of such values, the characteristic time of methyl rotation, appears to be a reliable sensor of interhelix contacts in transmembrane domains. The carbon NMR relaxation parameters of methyl groups can be measured accurately and with high sensitivity and resolution, making the proposed parameter a useful tool for investigation of protein-protein interfaces even in large membrane proteins. An approach to build the models of transmembrane dimers based on perturbations of methyl parameters and TMDOCK software is suggested.


    Organizational Affiliation

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997.,National Research Centre "Kurchatov Institute", Kurchatov Complex of NBICS-technologies, Akad. Kurchatova Sqr., 1, Moscow, Russian Federation, 123182. bon@nmr.ru.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, Str. Miklukho-Maklaya 16/10, Moscow, Russian Federation, 117997. bon@nmr.ru.,Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700.,Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudny, Russian Federation, 141700. bon@nmr.ru.,Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow, Russian Federation, 119991.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor tyrosine-protein kinase erbB-2
A, B
44Homo sapiensMutation(s): 0 
Gene Names: ERBB2 (HER2, MLN19, NEU, NGL)
EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens)
Go to Gene View: ERBB2
Go to UniProtKB:  P04626
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-14-00573

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Structure summary
  • Version 1.3: 2019-05-08
    Type: Data collection