PDBsum entry 2mjb

Signaling protein

PDB id: 2mjb

Contents

Protein chain

76 a.a.

PDB id:

2mjb

Name:

Signaling protein

Title:

Solution nmr structure of ubiquitin refined against dipolar couplings in 4 media

Structure:

Ubiquitin-60s ribosomal protein l40. Chain: a. Fragment: ubiquitin-like 3 domain. Synonym: cep52, ubiquitin a-52 residue ribosomal protein fusion product 1, ubiquitin, 60s ribosomal protein l40, ubiquitin-40s ribosomal protein s27a, ubiquitin carboxyl extension protein 80, ubiquitin, 40s ribosomal protein s27a, polyubiquitin-b, ubiquitin, polyubiquitin-c, ubiquitin. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: uba52, ubcep2, rps27a, uba80, ubcep1, ubb, ubc. Expressed in: escherichia coli. Expression_system_taxid: 511693.

NMR struc:

20 models

Authors:

A.Maltsev,A.Grishaev,J.Roche,M.Zasloff,A.Bax

Key ref:

A.S.Maltsev et al. (2014). Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase. J Am Chem Soc, 136, 3752-3755. PubMed id: 24568736 DOI: 10.1021/ja4132642

Date:

02-Jan-14 Release date: 26-Mar-14

Protein chain

P62987  (RL40_HUMAN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Homo sapiens

Seq: 128 a.a.

Struc: 76 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/ja4132642

J Am Chem Soc 136:3752-3755 (2014)

PubMed id: 24568736

Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.

A.S.Maltsev, A.Grishaev, J.Roche, M.Zasloff, A.Bax.

ABSTRACT

The antibiotic squalamine forms a lyotropic liquid crystal at very low concentrations in water (0.3-3.5% w/v), which remains stable over a wide range of temperature (1-40 °C) and pH (4-8). Squalamine is positively charged, and comparison of the alignment of ubiquitin relative to 36 previously reported alignment conditions shows that it differs substantially from most of these, but is closest to liquid crystalline cetyl pyridinium bromide. High precision residual dipolar couplings (RDCs) measured for the backbone (1)H-(15)N, (15)N-(13)C', (1)H(α)-(13)C(α), and (13)C'-(13)C(α) one-bond interactions in the squalamine medium fit well to the static structural model previously derived from NMR data. Inclusion into the structure refinement procedure of these RDCs, together with (1)H-(15)N and (1)H(α)-(13)C(α) RDCs newly measured in Pf1, results in improved agreement between alignment-induced changes in (13)C' chemical shift, (3)JHNHα values, and (13)C(α)-(13)C(β) RDCs and corresponding values predicted by the structure, thereby validating the high quality of the single-conformer structural model. This result indicates that fitting of a single model to experimental data provides a better description of the average conformation than does averaging over previously reported NMR-derived ensemble representations. The latter can capture dynamic aspects of a protein, thus making the two representations valuable complements to one another.