Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 158.49 kDa 
• Atom Count: 1452 
• Modelled Residue Count: 1452 
• Deposited Residue Count: 1452 
• Unique protein chains: 2

1ZVO

Semi-extended solution structure of human myeloma immunoglobulin D determined by constrained X-ray scattering

• PDB DOI: 10.2210/pdb1ZVO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2005-06-02 Released: 2005-10-25 
• Deposition Author(s): Sun, Z., Almogren, A., Furtado, P.B., Chowdhury, B., Kerr, M.A., Perkins, S.J.

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Experimental Data Snapshot

• Method: SOLUTION SCATTERING

Literature

Semi-extended Solution Structure of Human Myeloma Immunoglobulin D Determined by Constrained X-ray Scattering.

Sun, Z., Almogren, A., Furtado, P.B., Chowdhury, B., Kerr, M.A., Perkins, S.J.

(2005) J Mol Biol 353: 155-173

• PubMed: 16157351 
• DOI: 10.1016/j.jmb.2005.07.072
• Primary Citation of Related Structures:  
  1ZVO


• PubMed Abstract: 
  

Human immunoglobulin D (IgD) occurs most abundantly as a membrane-bound antibody on the surface of mature B cells (mIgD). IgD possesses the longest hinge sequence of all the human antibody isotypes, with 64 residues connecting the Fab and Fc fragments. A novel rapid purification scheme of secreted IgD from the serum of an IgD myeloma patient using thiophilic (T-gel) and lectin affinity chromatography gave a stable, homogeneous IgD preparation. Synchrotron X-ray scattering and analytical ultracentrifugation of IgD identified the solution arrangement of its Fab and Fc fragments, and thereby its hinge structure. The Guinier X-ray radius of gyration R(G) of 6.9(+/-0.1)nm showed that IgD is more extended in solution than the immunoglobulin subclass IgA1 (R(G) of 6.1-6.2nm). Its distance distribution function P(r) showed a single peak at 4.7nm and a maximum dimension of 23nm. Velocity experiments gave a sedimentation coefficient of 6.3S, which is similar to that for IgA1 at 6.2S. The complete IgD structure was modelled using molecular dynamics to generate IgD hinge structures, to which homology models for the Fab and Fc fragments were connected. Good scattering curve fits were obtained with 18 semi-extended best fit IgD models that were filtered from 8500 trial models. These best-fit models showed that the IgD hinge does not correspond to an extended polypeptide structure. The averaged solution structure arrangement of the Fab and Fc fragments in IgD is principally T-shaped and flexible, with contribution from Y-shaped and inverted Y-shaped structures. Although the linear sequence of the IgD hinge is much longer, comparison with previous scattering modelling of IgA1 and IgA2(m)1 suggests that the hinge of IgA1 and IgD are more similar than might have been expected, Both possess flexible T-shaped solution structures, probably reflecting the presence of restraining O-linked sugars.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Royal Free and University College Medical School, University College London, Gower Street, London WC1E 6BT, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
myeloma immunoglobulin D lambda	A, B	214	Homo sapiens	Mutation(s): 0  Gene Names: IGLC1, IGLV1-47
UniProt & NIH Common Fund Data Resources
Find proteins for P01700 (Homo sapiens) Explore P01700  Go to UniProtKB:  P01700
PHAROS:  P01700 GTEx:  ENSG00000211648
Find proteins for P0CG04 (Homo sapiens) Explore P0CG04  Go to UniProtKB:  P0CG04
UniProt Groups	P01700P0CG04

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin delta heavy chain	C, D	512	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX3 (Homo sapiens) Explore P0DOX3  Go to UniProtKB:  P0DOX3

Experimental Data & Validation

Experimental Data

• Method: SOLUTION SCATTERING

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-02 
• Released Date: 2005-10-25 
Deposition Author(s): Sun, Z., Almogren, A., Furtado, P.B., Chowdhury, B., Kerr, M.A., Perkins, S.J.

Revision History  

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-21
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2017-10-11
  Changes: Refinement description