Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 8.84 kDa 
• Atom Count: 602 
• Modelled Residue Count: 76 
• Deposited Residue Count: 79 
• Unique protein chains: 1

6QF8

Solution NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method

• PDB DOI: 10.2210/pdb6QF8/pdb
• BMRB: 34351

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-09 Released: 2019-04-10 
• Deposition Author(s): ElGamacy, M., Truffault, V., Zhu, H., Coles, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 20 
• Selection Criteria: NOESY-based R-factor selection 

Literature

Mapping Local Conformational Landscapes of Proteins in Solution.

ElGamacy, M., Riss, M., Zhu, H., Truffault, V., Coles, M.

(2019) Structure 27: 853-865.e5

• PubMed: 30930065 
• DOI: 10.1016/j.str.2019.03.005
• Primary Citation of Related Structures:  
  6QF8, 6QFP, 6QH2


• PubMed Abstract: 
  

The ability of proteins to adopt multiple conformational states is essential to their function, and elucidating the details of such diversity under physiological conditions has been a major challenge. Here we present a generalized method for mapping protein population landscapes by NMR spectroscopy. Experimental NOESY spectra are directly compared with a set of expectation spectra back-calculated across an arbitrary conformational space. Signal decomposition of the experimental spectrum then directly yields the relative populations of local conformational microstates. In this way, averaged descriptions of conformation can be eliminated. As the method quantitatively compares experimental and expectation spectra, it inherently delivers an R factor expressing how well structural models explain the input data. We demonstrate that our method extracts sufficient information from a single 3D NOESY experiment to perform initial model building, refinement, and validation, thus offering a complete de novo structure determination protocol.

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Organizational Affiliation: 

Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	79	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 20 
• Selection Criteria: NOESY-based R-factor selection 
• OLDERADO: 6QF8 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-01-09 
• Released Date: 2019-04-10 
Deposition Author(s): ElGamacy, M., Truffault, V., Zhu, H., Coles, M.

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references