PDBsum entry 1cdc

Immune system protein, receptor

PDB id

1cdc

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Contents

			Protein chains

					96 a.a. *

			Waters ×110

* Residue conservation analysis

PDB id:

1cdc

Links

Name:

Immune system protein, receptor

Title:

Cd2, n-terminal domain (1-99), truncated form

Structure:

Cd2. Chain: b, a. Synonym: lfa-2. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: pet

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å

R-factor:

0.192

Authors:

A.J.Murray,A.N.Barclay,R.L.Brady

Key ref:

A.J.Murray et al. (1995). One sequence, two folds: a metastable structure of CD2. Proc Natl Acad Sci U S A, 92, 7337-7341. PubMed id: 7638192 DOI: 10.1073/pnas.92.16.7337

Date:

23-May-95

Release date:

15-Sep-95

PROCHECK

	Headers

	References

Protein chains

P08921 (CD2_RAT) - T-cell surface antigen CD2 from Rattus norvegicus

Seq: Struc:					344 a.a. 96 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.?

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

DOI no: 10.1073/pnas.92.16.7337	Proc Natl Acad Sci U S A 92:7337-7341 (1995)
PubMed id: 7638192

One sequence, two folds: a metastable structure of CD2.
A.J.Murray, S.J.Lewis, A.N.Barclay, R.L.Brady.

ABSTRACT

When expressed as part of a glutathione S-transferase fusion protein the NH2-terminal domain of the lymphocyte cell adhesion molecule CD2 is shown to adopt two different folds. The immunoglobulin superfamily structure of the major (85%) monomeric component has previously been determined by both x-ray crystallography and NMR spectroscopy. We now describe the structure of a second, dimeric, form present in about 15% of recombinant CD2 molecules. After denaturation and refolding in the absence of the fusion partner, dimeric CD2 is converted to monomer, illustrating that the dimeric form represents a metastable folded state. The crystal structure of this dimeric form, refined to 2.0-A resolution, reveals two domains with overall similarity to the IgSF fold found in the monomer. However, in the dimer each domain is formed by the intercalation of two polypeptide chains. Hence each domain represents a distinct folding unit that can assemble in two different ways. In the dimer the two domains fold around a hydrophilic interface believed to mimic the cell adhesion interaction at the cell surface, and the formation of dimer can be regulated by mutating single residues at this interface. This unusual misfolded form of the protein, which appears to result from inter- rather than intramolecular interactions being favored by an intermediate structure formed during the folding process, illustrates that evolution of protein oligomers is possible from the sequence for a single protein domain.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20394753

A.F.Sonnen, C.Yu, E.J.Evans, D.I.Stuart, S.J.Davis, and R.J.Gilbert (2010).
Domain metastability: a molecular basis for immunoglobulin deposition?

J Mol Biol, 399, 207-213.

PDB code:

2x44

20630474

G.I.van Boxel, S.Holmes, L.Fugger, and E.Y.Jones (2010).
An alternative conformation of the T-cell receptor alpha constant region.

J Mol Biol, 400, 828-837.

PDB code:

3mff

19948502

E.Klaile, O.Vorontsova, K.Sigmundsson, M.M.Müller, B.B.Singer, L.G.Ofverstedt, S.Svensson, U.Skoglund, and B.Obrink (2009).
The CEACAM1 N-terminal Ig domain mediates cis- and trans-binding and is essential for allosteric rearrangements of CEACAM1 microclusters.

J Cell Biol, 187, 553-567.

18395225

S.Posy, L.Shapiro, and B.Honig (2008).
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?

J Mol Biol, 378, 954-968.

17426384

A.Pal, P.Chakrabarti, R.Bahadur, F.Rodier, and J.Janin (2007).
Peptide segments in protein-protein interfaces.

J Biosci, 32, 101-111.

17935152

S.Meier, and S.Ozbek (2007).
A biological cosmos of parallel universes: does protein structural plasticity facilitate evolution?

Bioessays, 29, 1095-1104.

17391511

V.Alva, M.Ammelburg, J.Söding, and A.N.Lupas (2007).
On the origin of the histone fold.

BMC Struct Biol, 7, 17.

16231289

H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.

Proteins, 61, 704-721.

15296726

M.J.Bennett, and D.Eisenberg (2004).
The evolving role of 3D domain swapping in proteins.

Structure, 12, 1339-1341.

15189881

S.Kundu, and R.L.Jernigan (2004).
Molecular mechanism of domain swapping in proteins: an analysis of slower motions.

Biophys J, 86, 3846-3854.

15326605

Y.H.Sanejouand (2004).
Domain swapping of CD4 upon dimerization.

Proteins, 57, 205-212.

12601793

G.A.Papoian, and P.G.Wolynes (2003).
The physics and bioinformatics of binding and folding-an energy landscape perspective.

Biopolymers, 68, 333-349.

11839489

M.E.Newcomer (2002).
Protein folding and three-dimensional domain swapping: a strained relationship?

Curr Opin Struct Biol, 12, 48-53.

12021428

Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.

Protein Sci, 11, 1285-1299.

11509370

J.G.Head, A.Houmeida, P.J.Knight, A.R.Clarke, J.Trinick, and R.L.Brady (2001).
Stability and folding rates of domains spanning the large A-band super-repeat of titin.

Biophys J, 81, 1570-1579.

11159452

M.S.Kellermayer, S.B.Smith, C.Bustamante, and H.L.Granzier (2001).
Mechanical fatigue in repetitively stretched single molecules of titin.

Biophys J, 80, 852-863.

11063574

N.Schiering, E.Casale, P.Caccia, P.Giordano, and C.Battistini (2000).
Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex.

Biochemistry, 39, 13376-13382.

PDB code:

1fyr

10508783

J.Clarke, E.Cota, S.B.Fowler, and S.J.Hamill (1999).
Folding studies of immunoglobulin-like beta-sandwich proteins suggest that they share a common folding pathway.

Structure, 7, 1145-1153.

10024022

V.Prasanna, B.Gopal, M.R.Murthy, D.V.Santi, and P.Balaram (1999).
Effect of amino acid substitutions at the subunit interface on the stability and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the Dimer interface of thymidylate synthase.

Proteins, 34, 356-368.

9731771

A.J.Murray, J.G.Head, J.J.Barker, and R.L.Brady (1998).
Engineering an intertwined form of CD2 for stability and assembly.

Nat Struct Biol, 5, 778-782.

PDB codes:

1a64 1a6p 1a7b

9671502

A.P.Saint-Jean, K.R.Phillips, D.J.Creighton, and M.J.Stone (1998).
Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping.

Biochemistry, 37, 10345-10353.

9702751

D.J.Goldstein (1998).
An unacknowledged problem for structural genomics?

Nat Biotechnol, 16, 696.

9541024

I.Hunter, K.Sigmundsson, N.Beauchemin, and B.Obrink (1998).
The cell adhesion molecule C-CAM is a substrate for tissue transglutaminase.

FEBS Lett, 425, 141-144.

9737871

K.M.Arndt, K.M.Müller, and A.Plückthun (1998).
Factors influencing the dimer to monomer transition of an antibody single-chain Fv fragment.

Biochemistry, 37, 12918-12926.

9666333

R.B.Russell, and C.P.Ponting (1998).
Protein fold irregularities that hinder sequence analysis.

Curr Opin Struct Biol, 8, 364-371.

9770640

S.M.Mockus, and K.E.Vrana (1998).
Advances in the molecular characterization of tryptophan hydroxylase.

J Mol Neurosci, 10, 163-179.

9442878

D.J.Leahy (1997).
Implications of atomic-resolution structures for cell adhesion.

Annu Rev Cell Dev Biol, 13, 363-393.

8989326

J.Lubkowski, G.Bujacz, L.Boqué, P.J.Domaille, T.M.Handel, and A.Wlodawer (1997).
The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions.

Nat Struct Biol, 4, 64-69.

PDB codes:

1dok 1dol

9153419

M.J.Parker, and A.R.Clarke (1997).
Amide backbone and water-related H/D isotope effects on the dynamics of a protein folding reaction.

Biochemistry, 36, 5786-5794.

9341233

M.J.Parker, C.E.Dempsey, M.Lorch, and A.R.Clarke (1997).
Acquisition of native beta-strand topology during the rapid collapse phase of protein folding.

Biochemistry, 36, 13396-13405.

8696971

A.D.Miranker, and C.M.Dobson (1996).
Collapse and cooperativity in protein folding.

Curr Opin Struct Biol, 6, 31-42.

8855243

K.W.Plaxco, C.Spitzfaden, I.D.Campbell, and C.M.Dobson (1996).
Rapid refolding of a proline-rich all-beta-sheet fibronectin type III module.

Proc Natl Acad Sci U S A, 93, 10703-10706.

8547253

R.A.Albright, M.C.Mossing, and B.W.Matthews (1996).
High-resolution structure of an engineered Cro monomer shows changes in conformation relative to the native dimer.

Biochemistry, 35, 735-742.

PDB code:

1orc

8749360

D.I.Stuart, and E.Y.Jones (1995).
Recognition at the cell surface: recent structural insights.

Curr Opin Struct Biol, 5, 735-743.

8580836

M.J.Bennett, M.P.Schlunegger, and D.Eisenberg (1995).
3D domain swapping: a mechanism for oligomer assembly.

Protein Sci, 4, 2455-2468.

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.