7WT3

Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structures of N-myristoylated lipopeptide-bound HLA class I complexes indicate reorganization of B-pocket architecture upon ligand binding.

Asa, M., Morita, D., Kuroha, J., Mizutani, T., Mori, N., Mikami, B., Sugita, M.

(2022) J Biol Chem : 102100-102100

  • DOI: 10.1016/j.jbc.2022.102100
  • Primary Citation of Related Structures:  
    7WJ2, 7WJ3, 7WT3, 7WT4, 7WT5

  • PubMed Abstract: 

    • Rhesus monkeys have evolved major histocompatibility complex (MHC)-encoded class I allomorphs such as Mamu-B*098 that are capable of binding N-myristoylated short lipopeptides rather than conventional long peptides; however, it remains unknown whether such antigen-binding molecules exist in other species, including humans ...

    Rhesus monkeys have evolved major histocompatibility complex (MHC)-encoded class I allomorphs such as Mamu-B*098 that are capable of binding N-myristoylated short lipopeptides rather than conventional long peptides; however, it remains unknown whether such antigen-binding molecules exist in other species, including humans. We herein demonstrate that human leukocyte antigen (HLA)-A*24:02 and HLA-C*14:02 proteins, which are known to bind conventional long peptides, also have the potential to bind N-myristoylated short lipopeptides. These HLA class I molecules shared a serine at position 9 (Ser9) with Mamu-B*098, in contrast to most MHC class I molecules that harbor a larger amino acid residue, such as tyrosine, at this position. High resolution X-ray crystallographic analyses of lipopeptide-bound HLA-A*24:02 and HLA-C*14:02 complexes indicated that Ser9 was at the bottom of the B pocket with its small hydroxymethyl side chain directed away from the B-pocket cavity, thereby contributing to the formation of a deep hydrophobic cavity suitable for accommodating the long-chain fatty acid moiety of lipopeptide ligands. Upon peptide binding, however, we found the hydrogen-bond network involving Ser9 was reorganized, and the remodeled B pocket was able to capture the second amino acid residue (P2) of peptide ligands. Apart from the B pocket, virtually no marked alterations were observed for the A and F pockets upon peptide and lipopeptide binding. Thus, we concluded that the structural flexibility of the large B pocket of HLA-A*2402 and HLA-C*1402 primarily accounted for their previously unrecognized capacity to bind such chemically distinct ligands as conventional peptides and N-myristoylated lipopeptides.

    Organizational Affiliation: 

    Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address: msugita@infront.kyoto-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigenA, D277Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A411J078 (Homo sapiens)
Explore A0A411J078 
Go to UniProtKB:  A0A411J078
Entity Groups  
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UniProt GroupA0A411J078
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
4-mer lipopeptideC, F5artificial sequencesMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS
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G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
ZN
Query on ZN
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J [auth A],
K [auth A],
MA [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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AA [auth A],
BA [auth A],
CA [auth A],
DA [auth B],
EA [auth B],
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
L [auth A],
M [auth A],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
SA [auth D],
T [auth A],
TA [auth D],
U [auth A],
UA [auth D],
V [auth A],
VA [auth D],
W [auth A],
WA [auth D],
X [auth A],
XA [auth E],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
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H [auth A],
I [auth A],
LA [auth D]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.069α = 90
b = 46.41β = 104.873
c = 142.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K07172
Japan Society for the Promotion of Science (JSPS)Japan21K07078
Japan Society for the Promotion of Science (JSPS)Japan20J23335
Japan Society for the Promotion of Science (JSPS)Japan19H04805
Japan Society for the Promotion of Science (JSPS)Japan21H02968
Japan Society for the Promotion of Science (JSPS)Japan20K21615
Japan Society for the Promotion of Science (JSPS)Japan19H04805
Japan Society for the Promotion of Science (JSPS)Japan18K19563
Japan Society for the Promotion of Science (JSPS)Japan18H02852

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release