PDBsum entry 1dcl

Immunoglobulin

PDB id

1dcl

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Contents

			Protein chains

					216 a.a. *

			Waters ×413

* Residue conservation analysis

PDB id:

1dcl

Links

Name:

Immunoglobulin

Title:

Mcg, a lambda v type light-chain dimer (bence-jones protein), crystallized from ammonium sulfate

Structure:

Mcg. Chain: a, b. Synonym: bence-jones protein. Other_details: a lambda v type light-chain dimer

Source:

Homo sapiens. Human. Organism_taxid: 9606

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å

R-factor:

0.140

Authors:

M.Schiffer,Z.B.Xu

Key ref:

K.R.Ely et al. (1989). Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms. J Mol Biol, 210, 601-615. PubMed id: 2515285

Date:

16-Oct-95

Release date:

15-May-97

PROCHECK

	Headers

	References

Protein chains

P01709 (LV208_HUMAN) - Immunoglobulin lambda variable 2-8 from Homo sapiens

Seq: Struc:					118 a.a. 216 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

	J Mol Biol 210:601-615 (1989)
PubMed id: 2515285

Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms.
K.R.Ely, J.N.Herron, M.Harker, A.B.Edmundson.

ABSTRACT

The three-dimensional structure of an immunoglobulin light chain dimer (Mcg) crystallized in deionized water (orthorhombic form) was determined at 2.0 A resolution by phase extension and crystallographic refinement. This structure was refined side-by-side with that of the same molecule crystallized in ammonium sulfate (trigonal form). The dimer adopted markedly different structures in the two solvents. "Elbow bend" angles between pseudo 2-fold axes of rotation relating pairs of "variable" (V) and "constant" (C) domains were found to be 132 degrees in the orthorhombic form and 115 degrees in the trigonal form. Modes of association of the V domains and, to a lesser extent, the pairing interactions of the C domains were different in the two structures. Alterations in the V domain pairing were reflected in the shapes of the binding regions and in the orientations of the side-chains lining the walls of the binding sites. In the trigonal form, for instance, the V domain interface was compartmentalized into a main binding cavity and a deep pocket, whereas these spaces were continuous in the orthorhombic structure. Patterns of ordered water molecules were quite distinct in the two crystal types. In some cases, the solvent structures could be correlated with conformational changes in the proteins. For example, close contacts between V and C domains of monomer 1 of the trigonal form were not retained in orthorhombic crystals. Ordered water molecules filled the space created when the two domains moved apart.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20737441

D.Pednekar, and S.Durani (2010).
Protein homomers in point-group assembly: symmetry making and breaking are specific and distinctive in their codes of chemical alphabet in side chains.

Proteins, 78, 3048-3055.

19546861

Y.Levin, L.Wang, E.Schwarz, D.Koethe, F.M.Leweke, and S.Bahn (2010).
Global proteomic profiling reveals altered proteomic signature in schizophrenia serum.

Mol Psychiatry, 15, 1088-1100.

18080994

F.J.Stevens (2008).
Homology versus analogy: possible evolutionary relationship of immunoglobulins, cupredoxins, and Cu,Zn-superoxide dismutase.

J Mol Recognit, 21, 20-29.

17582169

D.L.Makino, A.H.Henschen-Edman, S.B.Larson, and A.McPherson (2007).
Bence Jones KWR protein structures determined by X-ray crystallography.

Acta Crystallogr D Biol Crystallogr, 63, 780-792.

PDB codes:

2old 2omb 2omn

16508097

D.L.Makino, A.H.Henschen-Edman, and A.McPherson (2005).
Four crystal forms of a Bence-Jones protein.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 79-82.

12447911

E.Yuriev, and P.A.Ramsland (2002).
Mcg light chain dimer as a model system for ligand design: a docking study.

J Mol Recognit, 15, 331-340.

12447901

P.A.Ramsland, and W.Farrugia (2002).
Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products.

J Mol Recognit, 15, 248-259.

11976493

P.C.Bourne, P.A.Ramsland, L.Shan, Z.C.Fan, C.R.DeWitt, B.B.Shultz, S.S.Terzyan, C.R.Moomaw, C.A.Slaughter, L.W.Guddat, and A.B.Edmundson (2002).
Three-dimensional structure of an immunoglobulin light-chain dimer with amyloidogenic properties.

Acta Crystallogr D Biol Crystallogr, 58, 815-823.

PDB code:

1jvk

11301481

J.J.Marchalonis, M.K.Adelman, I.F.Robey, S.F.Schluter, and A.B.Edmundson (2001).
Exquisite specificity and peptide epitope recognition promiscuity, properties shared by antibodies from sharks to humans.

J Mol Recognit, 14, 110-121.

10739264

T.M.Weaver (2000).
The pi-helix translates structure into function.

Protein Sci, 9, 201-206.

10091599

A.Roussel, S.Spinelli, S.Déret, J.Navaza, P.Aucouturier, and C.Cambillau (1999).
The structure of an entire noncovalent immunoglobulin kappa light-chain dimer (Bence-Jones protein) reveals a weak and unusual constant domains association.

Eur J Biochem, 260, 192-199.

PDB code:

1b6d

9630831

A.B.Edmundson, and C.V.Manion (1998).
Treatment of osteoarthritis with aspartame.

Clin Pharmacol Ther, 63, 580-593.

PDB code:

1a8j

7971973

D.F.Lake, S.F.Schluter, E.Wang, R.M.Bernstein, A.B.Edmundson, and J.J.Marchalonis (1994).
Autoantibodies to the alpha/beta T-cell receptors in human immunodeficiency virus infection: dysregulation and mimicry.

Proc Natl Acad Sci U S A, 91, 10849-10853.

7704530

D.I.Liao, and O.Herzberg (1994).
Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins.

Structure, 2, 1203-1216.

PDB codes:

1sph 2hpr

7536111

I.A.Wilson, and R.L.Stanfield (1994).
Antibody-antigen interactions: new structures and new conformational changes.

Curr Opin Struct Biol, 4, 857-867.

8346191

A.B.Edmundson, D.L.Harris, Z.C.Fan, L.W.Guddat, B.T.Schley, B.L.Hanson, G.Tribbick, and H.M.Geysen (1993).
Principles and pitfalls in designing site-directed peptide ligands.

Proteins, 16, 246-267.

PDB codes:

1mcb 1mcc 1mcd 1mce 1mcf 1mch 1mci 1mcj 1mck 1mcl 1mcn 1mcq 1mcr 1mcs

8136016

H.Kaymaz, and J.J.Marchalonis (1993).
Autoreactive sites of human lambda light chain mapped by comprehensive peptide synthesis.

J Protein Chem, 12, 659-666.

8483943

L.W.Guddat, J.N.Herron, and A.B.Edmundson (1993).
Three-dimensional structure of a human immunoglobulin with a hinge deletion.

Proc Natl Acad Sci U S A, 90, 4271-4275.

PDB code:

1mco

1384034

C.Eigenbrot, M.Randal, and A.A.Kossiakoff (1992).
Structural effects induced by mutagenesis affected by crystal packing factors: the structure of a 30-51 disulfide mutant of basic pancreatic trypsin inhibitor.

Proteins, 14, 75-87.

PDB code:

1aal

1382435

J.J.Marchalonis, F.Dedeoglu, H.Kaymaz, S.F.Schluter, and A.B.Edmundson (1992).
Antigenic mapping of a human lambda light chain: correlation with three dimensional structure.

J Protein Chem, 11, 129-137.

1565623

J.J.Marchalonis, H.Kaymaz, F.Dedeoglu, S.F.Schluter, D.E.Yocum, and A.B.Edmundson (1992).
Human autoantibodies reactive with synthetic autoantigens from T-cell receptor beta chain.

Proc Natl Acad Sci U S A, 89, 3325-3329.

1367864

A.Plückthun (1991).
Antibody engineering.

Curr Opin Biotechnol, 2, 238-246.

2062826

J.A.Bell, K.P.Wilson, X.J.Zhang, H.R.Faber, H.Nicholson, and B.W.Matthews (1991).
Comparison of the crystal structure of bacteriophage T4 lysozyme at low, medium, and high ionic strengths.

Proteins, 10, 10-21.

PDB codes:

4lzm 5lzm 6lzm 7lzm

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 codes are shown on the right.