8EC5: MHC class I antigen

Structures of HLA-B8E76C loaded with long peptides reveal novel features at the N-terminus of the groove. Determined by X-ray diffraction at 1.22 Å resolution. Released 26 Jul 2023.

Method: X-ray diffraction
Resolution: 1.22 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 3
Atoms: 3,356
Mol. weight: 46.05 kDa
Released: 26 Jul 2023

Explore 8EC5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EC5 contains 16 α-helices and 29 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
α-helix	61-84	24
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
α-helix	182	1
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	Q5SS57 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
peptide RARARARARARAFVKKKYCL	C	protein	20	Human immunodeficiency virus 1

Sequence of entity 1 (A), FASTA

>8EC5_1 MHC class I antigen (chains A)
GSHSMRYFDTAMSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW
DRNTQIFKTNTQTDRCSLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHNQYAYDG
KDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQDRAYLEGTCVEWLRRYLENGKDTLE
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>8EC5_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8EC5_3 peptide RARARARARARAFVKKKYCL (chains C)
RARARARARARAFVKKKYCL

Primary citation

Crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing. Li, L., Peng, X., Batliwala, M. et al. Nat Commun (2023) 14:5020-5020. DOI 10.1038/s41467-023-40736-6 · PubMed

Other PDB entries of the same protein (UniProt Q5SS57 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8E2Z 1.13 Å, Structures of HLA-B8E76C loaded with long peptides reveal novel features at the…
8E13 1.37 Å, Structures of HLA-B8E76C loaded with long peptides reveal novel features at the…
8E8I 1.49 Å, Structures of HLA-B8E76C loaded with long peptides reveal novel features at the…

Browse structure collections

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