3MCG

THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report



Literature

Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms.

Ely, K.R.Herron, J.N.Harker, M.Edmundson, A.B.

(1989) J Mol Biol 210: 601-615

  • DOI: 10.1016/0022-2836(89)90135-6
  • Primary Citation of Related Structures:  
    3MCG, 2MCG, 1DCL

  • PubMed 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 ...

    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.


    Related Citations: 
    • The Binding of Opioid Peptides to the Mcg Light Chain Dimer. Flexible Keys and Adjustable Locks
      Edmundson, A.B., Ely, K.R., Herron, J.N., Cheson, B.D.
      (1987) Mol Immunol 24: 915
    • Three-Dimensional Structure of the Orthorhombic Form of the Mcg Bence-Jones Dimer
      Ely, K.R., Herron, J.N., Edmundson, A.B.
      (1983) Progress In Immunology V --: 61
    • Small-Angle Neutron Scattering Study of Bence-Jones Protein Mcg. Comparison of Structures in Solution and in Crystal
      Schiffer, M., Stevens, F.J., Westholm, F.A., Kim, S.S., Carlson, R.D.
      (1982) Biochemistry 21: 2874
    • Marked Structural Differences of the Mcg Bence-Jones Dimer in Two Crystal Systems
      Abola, E.E., Ely, K.R., Edmundson, A.B.
      (1980) Biochemistry 19: 432
    • Crystal Properties as Indicators of Conformational Changes During Ligand Binding or Interconversion of Mcg Light Chain Isomers
      Ely, K.R., Firca, J.R., Williams, K.J., Abola, E.E., Fenton, J.M., Schiffer, M., Panagiotopoulos, N.C., Edmundson, A.B.
      (1978) Biochemistry 17: 158
    • Interconversion of Conformational Isomers of Light Chains in the Mcg Immunoglobulins
      Firca, J.R., Ely, K.R., Kremser, P., Westholm, F.A., Dorrington, K.J., Edmundson, A.B.
      (1978) Biochemistry 17: 148
    • The Antibody Combining Site
      Capra, J.D., Edmundson, A.B.
      (1977) Sci Am 236: 50
    • Implications of Conformational Isomerism and Rotational Allomerism to the Binding of Small Molecules by the Mcg Bence-Jones Dimer
      Edmundson, A.B., Abola, E.E., Ely, K.R., Firca, J.R., Panagiotopoulos, N.C., Schiffer, M., Westholm, F.A.
      (1977) Antibodies In Human Diagnosis And Therapy --: 135
    • Conformational Isomerism,Rotational Allomerism, and Divergent Evolution in Immunoglobulin Light Chains
      Edmundson, A.B., Ely, K.R., Abola, E.E., Schiffer, M., Panagiotopoulos, N., Deutsch, H.F.
      (1976) Fed Proc 35: 2119
    • Rotational Allomerism and Divergent Evolution of Domains in Immunoglobulin Light Chains
      Edmundson, A.B., Ely, K.R., Abola, E.E., Schiffer, M., Panagiotopoulos, N.
      (1975) Biochemistry 14: 3953
    • Binding of 2,4-Dinitrophenyl Compounds and Other Small Molecules to a Crystalline Lambda-Type Bence-Jones Dimer
      Edmundson, A.B., Ely, K.R., Girling, R.L., Abola, E.E., Schiffer, M., Westholm, F.A., Fausch, M.D., Deutsch, H.F.
      (1974) Biochemistry 13: 3816
    • Structure and Binding Properties of a Lambda-Type Bence-Jones Dimer
      Edmundson, A.B., Ely, K.R., Girling, R.L., Abola, E.E., Schiffer, M., Westholm, F.A.
      (1974) Progress In Immunology Ii 1: 103
    • Primary Structure of the Mcg Lambda Chain
      Fett, J.W., Deutsch, H.F.
      (1974) Biochemistry 13: 4102
    • Preparation and Properties of a Bence-Jones Dimer with Mercury Inserted Into the Interchain Disulfide Bond
      Ely, K.R., Girling, R.L., Schiffer, M., Cunningham, D.E., Edmundson, A.B.
      (1973) Biochemistry 12: 4233
    • Structure of a Lambda-Type Bence-Jones Protein at 3.5-Angstroms Resolution
      Schiffer, M., Girling, R.L., Ely, K.R., Edmundson, A.B.
      (1973) Biochemistry 12: 4620
    • Structural Features of Immunoglobulin Light Chains
      Edmundson, A.B., Schiffer, M., Ely, K.R., Wood, M.K.
      (1973) Prog Mol Subcell Biol 3: 159
    • Structure of a Lambda-Type Bence-Jones Protein at 6-Angstroms Resolution
      Edmundson, A.B., Schiffer, M., Ely, K.R., Wood, M.K.
      (1972) Biochemistry 11: 1822
    • Crystallographic Studies of an Igg Immunoglobulin and the Bence-Jones Protein from One Patient
      Edmundson, A.B., Schiffer, M., Wood, M.K., Hardman, K.D., Ely, K.R., Ainsworth, C.F.
      (1972) Cold Spring Harb Symp Quant Biol 36: 427

    Organizational Affiliation

    Department of Biology, University of Utah, Salt Lake City 84112.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)12216Homo sapiensMutation(s): 0 
Gene Names: IGLV2-8
Find proteins for P01709 (Homo sapiens)
Explore P01709 
Go to UniProtKB:  P01709
NIH Common Fund Data Resources
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
1,2L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.8α = 90
b = 81.9β = 90
c = 71γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Other, Polymer sequence