Alpha This is a work in progress and may change. Your feedback is very welcome.
  


4N0F

Non-classical MHC Class I molecule Feonatal Fc receptor (FcRn) with serum albumin at 3.02Å 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 beta2m and serum albumin

1. Beta 2 microglobulin
['B', 'F', 'I', 'L']
2. Fc receptor (FcRn)
['A', 'E', 'H', 'K']
3. Serum Albumin
['D', 'G', 'J', 'M']

Species


Locus / Allele group

Non-classical MHC Class I molecule

Publication

Structural Insights into Neonatal Fc Receptor-based Recycling Mechanisms.

Oganesyan V, Damschroder MM, Cook KE, Li Q, Gao C, Wu H, Dall'Acqua WF
J. Biol. Chem. (2014) 289, 7812-24 [doi:10.1074/jbc.M113.537563]  [pubmed:24469444

We report the three-dimensional structure of human neonatal Fc receptor (FcRn) bound concurrently to its two known ligands. More particularly, we solved the crystal structure of the complex between human FcRn, wild-type human serum albumin (HSA), and a human Fc engineered for improved pharmacokinetics properties (Fc-YTE). The crystal structure of human FcRn bound to wild-type HSA alone is also presented. HSA domain III exhibits an extensive interface of contact with FcRn, whereas domain I plays a lesser role. A molecular explanation for the HSA recycling mechanism is provided with the identification of FcRn His(161) as the only potential direct contributor to the corresponding pH-dependent process. At last, this study also allows an accurate structural definition of residues considered for decades as important to the human IgG/FcRn interaction and reveals Fc His(310) as a significant contributor to pH-dependent binding. Finally, we explain various structural mechanisms by which several Fc mutations (including YTE) result in increased human IgG binding to FcRn. Our study provides an unprecedented relevant understanding of the molecular basis of human Fc interaction with human FcRn.

Structure deposition and release

Deposited: 2013-10-01
Released: 2014-02-05
Revised: 2014-04-09

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Fc receptor (FcRn)
Fc receptor (FcRn)
        10        20        30        40        50        60
HLSLLYHLTAVSSPAPGTPAFWVSGWLGPQQYLSYNSLRGEAEPCGAWVWENQVSWYWEK
        70        80        90       100       110       120
ETTDLRIKEKLFLEAFKALGGKGPYTLQGLLGCELGPDNTSVPTAKFALNGEEFMNFDLK
       130       140       150       160       170       180
QGTWGGDWPEALAISQRWQQQDKAANKELTFLLFSCPHRLREHLERGRGNLEWKEPPSMR
       190       200       210       220       230       240
LKARPSSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGTGQGDFGPNSDGSFHASSSLTVK
       250       260       270
SGDEHHYCCIVQHAGLAQPLRVELESPAKSS

3. Serum Albumin
Serum Albumin
        10        20        30        40        50        60
DAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAE
        70        80        90       100       110       120
NCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEV
       130       140       150       160       170       180
DVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLP
       190       200       210       220       230       240
KLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTK
       250       260       270       280       290       300
VHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPA
       310       320       330       340       350       360
DLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKC
       370       380       390       400       410       420
CAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVST
       430       440       450       460       470       480
PTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTES
       490       500       510       520       530       540
LVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKAT
       550       560       570       580
KEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL


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.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:
   e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif
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. 4N0F assembly 1  
  2. 4N0F assembly 2  
  3. 4N0F assembly 3  
  4. 4N0F assembly 4  

Components

MHC Class I alpha chain [cif]
  1. 4N0F assembly 1  
  2. 4N0F assembly 2  
  3. 4N0F assembly 3  
  4. 4N0F assembly 4  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 4N0F assembly 1  
  2. 4N0F assembly 2  
  3. 4N0F assembly 3  
  4. 4N0F assembly 4  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/4n0f

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