5KNM

Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with NK-cell receptors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.303 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human Leukocyte Antigen F Presents Peptides and Regulates Immunity through Interactions with NK Cell Receptors.

Dulberger, C.L.McMurtrey, C.P.Holzemer, A.Neu, K.E.Liu, V.Steinbach, A.M.Garcia-Beltran, W.F.Sulak, M.Jabri, B.Lynch, V.J.Altfeld, M.Hildebrand, W.H.Adams, E.J.

(2017) Immunity 46: 1018-1029.e7

  • DOI: 10.1016/j.immuni.2017.06.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Evidence is mounting that the major histocompatibility complex (MHC) molecule HLA-F (human leukocyte antigen F) regulates the immune system in pregnancy, infection, and autoimmunity by signaling through NK cell receptors (NKRs). We present structural ...

    Evidence is mounting that the major histocompatibility complex (MHC) molecule HLA-F (human leukocyte antigen F) regulates the immune system in pregnancy, infection, and autoimmunity by signaling through NK cell receptors (NKRs). We present structural, biochemical, and evolutionary analyses demonstrating that HLA-F presents peptides of unconventional length dictated by a newly arisen mutation (R62W) that has produced an open-ended groove accommodating particularly long peptides. Compared to empty HLA-F open conformers (OCs), HLA-F tetramers bound with human-derived peptides differentially stained leukocytes, suggesting peptide-dependent engagement. Our in vitro studies confirm that NKRs differentiate between peptide-bound and peptide-free HLA-F. The complex structure of peptide-loaded β2m-HLA-F bound to the inhibitory LIR1 revealed similarities to high-affinity recognition of the viral MHC-I mimic UL18 and a docking strategy that relies on contacts with HLA-F as well as β2m, thus precluding binding to HLA-F OCs. These findings provide a biochemical framework to understand how HLA-F could regulate immunity via interactions with NKRs.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cDNA FLJ39643 fis, clone SMINT2004023, highly similar to HLA class I histocompatibility antigen, alphachain F
A
284Homo sapiensMutation(s): 0 
Gene Names: HLA-F (HLA-5.4, HLAF)
Find proteins for P30511 (Homo sapiens)
Go to Gene View: HLA-F
Go to UniProtKB:  P30511
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
182Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Leukocyte immunoglobulin-like receptor subfamily B member 1
D
267Homo sapiensMutation(s): 0 
Gene Names: LILRB1 (ILT2, LIR1, MIR7)
Find proteins for Q8NHL6 (Homo sapiens)
Go to Gene View: LILRB1
Go to UniProtKB:  Q8NHL6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Peptide ILE-LEU-ARG-TRP-GLU-GLN
N
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.303 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 231.820α = 90.00
b = 231.820β = 90.00
c = 73.250γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI073922

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence