PDBsum entry 2k5x

Immune system/hydrolase

PDB id

2k5x

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Contents

			Protein chains

					86 a.a. *


					134 a.a. *

* Residue conservation analysis

PDB id:

2k5x

Links
- PDBe
- RCSB
- MMDB
- JenaLib
- Proteopedia
- CATH
- SCOP
- PDBSWS
- CSA
- ProSAT

Name:

Immune system/hydrolase

Title:

Chemical shift structure of colicin e9 dnase domain with its cognate immunity protein im9

Structure:

Colicin-e9 immunity protein. Chain: a. Synonym: imme9, microcin-e9 immunity protein. Engineered: yes. Colicin-e9. Chain: b. Fragment: unp residues 450-582. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: imm, ceie9. Expressed in: escherichia coli. Gene: col, cei. Expressed in: escherichia coli

NMR struc:

1 models

Authors:

R.W.Montalvao,A.Cavalli,M.Vendruscolo

Key ref:

R.W.Montalvao et al. (2008). Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex. J Am Chem Soc, 130, 15990-15996. PubMed id: 18980319

Date:

01-Jul-08

Release date:

09-Dec-08

PROCHECK

	Headers

	References

Protein chain

P13479 (IMM9_ECOLX) - Colicin-E9 immunity protein from Escherichia coli

Seq: Struc:					86 a.a. 86 a.a.

Protein chain

P09883 (CEA9_ECOLX) - Colicin-E9 from Escherichia coli

Seq: Struc:

Seq: Struc:					582 a.a. 134 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)



		Enzyme reactions

Enzyme class:

Chain B: E.C.3.1.-.-

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	J Am Chem Soc 130:15990-15996 (2008)
PubMed id: 18980319

Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex.
R.W.Montalvao, A.Cavalli, X.Salvatella, T.L.Blundell, M.Vendruscolo.

ABSTRACT

Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein-protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein-protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21483987

N.Rawat, and P.Biswas (2011).
Shape, flexibility and packing of proteins and nucleic acids in complexes.

Phys Chem Chem Phys, 13, 9632-9643.

19942687

J.Abi-Ghanem, B.Heddi, N.Foloppe, and B.Hartmann (2010).
DNA structures from phosphate chemical shifts.

Nucleic Acids Res, 38, e18.

20715051

J.H.Tomlinson, V.L.Green, P.J.Baker, and M.P.Williamson (2010).
Structural origins of pH-dependent chemical shifts in the B1 domain of protein G.

Proteins, 78, 3000-3016.

PDB code:

3mp9

20696393

P.Robustelli, K.Kohlhoff, A.Cavalli, and M.Vendruscolo (2010).
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins.

Structure, 18, 923-933.

20718048

S.J.de Vries, A.S.Melquiond, P.L.Kastritis, E.Karaca, A.Bordogna, M.van Dijk, J.P.Rodrigues, and A.M.Bonvin (2010).
Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.

Proteins, 78, 3242-3249.

19864631

R.Das, I.André, Y.Shen, Y.Wu, A.Lemak, S.Bansal, C.H.Arrowsmith, T.Szyperski, and D.Baker (2009).
Simultaneous prediction of protein folding and docking at high resolution.

Proc Natl Acad Sci U S A, 106, 18978-18983.

19081052

P.Robustelli, A.Cavalli, and M.Vendruscolo (2008).
Determination of protein structures in the solid state from NMR chemical shifts.

Structure, 16, 1764-1769.

PDB code:

2k0p

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.