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5WHK

Non-classical MHC Class I molecule Feonatal Fc receptor (FcRn) with antibody at 2.50Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Fcrn with antibody

1. ab_heavy
['H']
2. ab_light
['L']
3. Beta 2 microglobulin
['B']
4. Fc receptor (FcRn)
['A']

Species


Locus / Allele group

Non-classical MHC Class I molecule

Publication

Structural basis for pH-insensitive inhibition of immunoglobulin G recycling by an anti-neonatal Fc receptor antibody.

Kenniston JA, Taylor BM, Conley GP, Cosic J, Kopacz KJ, Lindberg AP, Comeau SR, Atkins K, Bullen J, TenHoor C, Adelman BA, Sexton DJ, Edwards TE, Nixon AE
J. Biol. Chem. (2017) 292, 17449-17460 [doi:10.1074/jbc.M117.807396]  [pubmed:28878017

The neonatal Fc receptor FcRn plays a critical role in the trafficking of IgGs across tissue barriers and in retaining high circulating concentrations of both IgG and albumin. Although generally beneficial from an immunological perspective in maintaining IgG populations, FcRn can contribute to the pathogenesis of autoimmune disorders when an abnormal immune response targets normal biological components. We previously described a monoclonal antibody (DX-2507) that binds to FcRn with high affinity at both neutral and acidic pH, prevents the simultaneous binding of IgG, and reduces circulating IgG levels in preclinical animal models. Here, we report a 2.5 Å resolution X-ray crystal structure of an FcRn-DX-2507 Fab complex, revealing a nearly complete overlap of the IgG-Fc binding site in FcRn by complementarity-determining regions in DX-2507. This overlap explains how DX-2507 blocks IgG binding to FcRn and thereby shortens IgG half-life by preventing IgGs from recycling back into circulation. Moreover, the complex structure explains how the DX-2507 interaction is pH-insensitive unlike normal Fc interactions and how serum albumin levels are unaffected by DX-2507 binding. These structural studies could inform antibody-based therapeutic approaches for limiting the effects of IgG-mediated autoimmune disease.

Structure deposition and release

Deposited: 2017-07-17
Released: 2017-09-06
Revised: 2018-03-21

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Chain sequences

1. ab_heavy
ab_heavy
        10        20        30        40        50        60
EVQLLESGGGLVQPGGSLRLSCAASGFTFSEYAMGWVRQAPGKGLEWVSSIGSSGGQTKY
        70        80        90       100       110       120
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARLAIGDSYWGQGTMVTVSSASTK
       130       140       150       160       170       180
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
       190       200       210
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

2. ab_light
ab_light
        10        20        30        40        50        60
QSALTQPASVSGSPGQSITISCTGTGSDVGSYNLVSWYQQHPGKAPKLMIYGDSQRPSGV
        70        80        90       100       110       120
SNRFSGSKSGNTASLTISGLQAEDEADYYCASYAGSGIYVFGTGTKVTVLGQPKANPTVT
       130       140       150       160       170       180
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASS
       190       200       210
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

3. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
MSRSVALAVLALLSLSGLEAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLL
        70        80        90       100       110
KNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

4. Fc receptor (FcRn)
Fc receptor (FcRn)
        10        20        30        40        50        60
MGVPRPQPWALGLLLFLLPGSLGAESHLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLS
        70        80        90       100       110       120
YNSLRGEAEPCGAWVWENQVSWYWEKETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCE
       130       140       150       160       170       180
LGPDNTSVPTAKFALNGEEFMNFDLKQGTWGGDWPEALAISQRWQQQDKAANKELTFLLF
       190       200       210       220       230       240
SCPHRLREHLERGRGNLEWKEPPSMRLKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGL
       250       260       270       280       290
AAGTGQGDFGPNSDGSFHASSSLTVKSGDEHHYCCIVQHAGLAQPLRVELESPAKSS


Data provenance

Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.


Downloadable data

Data can be downloaded to your local machine from the links below.
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or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 5WHK assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5WHK assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5WHK assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5whk

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes