6V5D

EROS3 RDC and NOE Derived Ubiquitin Ensemble

PDB DOI: 10.2210/pdb6V5D/pdb
BMRB: 30693

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

Deposited: 2019-12-04 Released: 2020-01-01
Deposition Author(s): Lange, O.F., Lakomek, N.A., Smith, C.A., Griesinger, C., de Groot, B.L.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 800
Conformers Submitted: 176
Selection Criteria: target function

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2K39

Literature

Enhancing NMR derived ensembles with kinetics on multiple timescales.

Smith, C.A., Mazur, A., Rout, A.K., Becker, S., Lee, D., de Groot, B.L., Griesinger, C.

(2020) J Biomol NMR 74: 27-43

PubMed: 31838619 Search on PubMedSearch on PubMed Central
DOI: 10.1007/s10858-019-00288-8
Primary Citation of Related Structures:
6V5D

PubMed Abstract:

Nuclear magnetic resonance (NMR) has the unique advantage of elucidating the structure and dynamics of biomolecules in solution at physiological temperatures, where they are in constant movement on timescales from picoseconds to milliseconds. Such motions have been shown to be critical for enzyme catalysis, allosteric regulation, and molecular recognition. With NMR being particularly sensitive to these timescales, detailed information about the kinetics can be acquired. However, nearly all methods of NMR-based biomolecular structure determination neglect kinetics, which introduces a large approximation to the underlying physics, limiting both structural resolution and the ability to accurately determine molecular flexibility. Here we present the Kinetic Ensemble approach that uses a hierarchy of interconversion rates between a set of ensemble members to rigorously calculate Nuclear Overhauser Effect (NOE) intensities. It can be used to simultaneously refine both temporal and structural coordinates. By generalizing ideas from the extended model free approach, the method can analyze the amplitudes and kinetics of motions anywhere along the backbone or side chains. Furthermore, analysis of a large set of crystal structures suggests that NOE data contains a surprising amount of high-resolution information that is better modeled using our approach. The Kinetic Ensemble approach provides the means to unify numerous types of experiments under a single quantitative framework and more fully characterize and exploit kinetically distinct protein states. While we apply the approach here to the protein ubiquitin and cross validate it with previously derived datasets, the approach can be applied to any protein for which NOE data is available.

Related Citations:

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.
Lange, O.F., Lakomek, N.A., Fares, C., Schroeder, G.F., Walter, K.F., Becker, S., Meiler, J., Grubmueller, H., Griesinger, C., de Groot, B.L.
(2008) Science 320: 1471

Organizational Affiliation:

Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. cigr@nmr.mpibpc.mpg.de.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0 Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG48
Protein Feature View Expand
Reference Sequence