8OJT

Crystal structure of the human IgD Fab - structure Fab2

PDB DOI: https://doi.org/10.2210/pdb8OJT/pdb

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

Deposited: 2023-03-24 Released: 2023-06-14
Deposition Author(s): Davies, A.M., Beavil, R.L., McDonnell, J.M.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.198
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structures of the human IgD Fab reveal insights into C H 1 domain diversity.

Davies, A.M., Beavil, R.L., Barbolov, M., Sandhar, B.S., Gould, H.J., Beavil, A.J., Sutton, B.J., McDonnell, J.M.

(2023) Mol Immunol 159: 28-37

PubMed: 37267832 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.molimm.2023.05.006
Primary Citation of Related Structures:
8OJS, 8OJT, 8OJU, 8OJV

PubMed Abstract:
Antibodies of the IgD isotype remain the least well characterized of the mammalian immunoglobulin isotypes. Here we report three-dimensional structures for the Fab region of IgD, based on four different crystal structures, at resolutions of 1.45-2.75 Å. These IgD Fab crystals provide the first high-resolution views of the unique Cδ1 domain. Structural comparisons identify regions of conformational diversity within the Cδ1 domain, as well as among the homologous domains of Cα1, Cγ1 and Cμ1. The IgD Fab structure also possesses a unique conformation of the upper hinge region, which may contribute to the overall disposition of the very long linker sequence between the Fab and Fc regions found in human IgD. Structural similarities observed between IgD and IgG, and differences with IgA and IgM, are consistent with predicted evolutionary relationships for the mammalian antibody isotypes.

Organizational Affiliation

King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom.

Macromolecule Content

Total Structure Weight: 48.96 kDa
Atom Count: 3,853
Modelled Residue Count: 442
Deposited Residue Count: 444
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human IgD Fab light chain	A [auth L]	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human IgD Fab heavy chain	B [auth H]	227	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H]	O [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H]	E [auth L] F [auth L] G [auth L] K [auth H] L [auth H] E [auth L], F [auth L], G [auth L], K [auth H], L [auth H], M [auth H], N [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain C [auth L] SDF format, chain H MOL2 format, chain C [auth L] MOL2 format, chain H	C [auth L], H	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Focus chain H Interactions & Density Focus chain C [auth L] Focus chain H
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain J [auth H] MOL2 format, chain D [auth L] MOL2 format, chain J [auth H]	D [auth L], J [auth H]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain J [auth H] Interactions & Density Focus chain D [auth L] Focus chain J [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth H] MOL2 format, chain I [auth H]	I [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]