7LGT: HLA-B*07:02

HLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83. Determined by X-ray diffraction at 1.97 Å resolution. Released 21 Apr 2021.

Method: X-ray diffraction
Resolution: 1.97 Å
Organisms: Homo sapiens, Human coronavirus 229E
Chains: 6
Atoms: 6,870
Mol. weight: 92.24 kDa
Ligands: ZN
Released: 21 Apr 2021

Explore 7LGT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LGT contains 22 α-helices and 60 β-strands across 4 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
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	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-180	5
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
β-strand	228-230	3	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

Chains B and D: 2 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
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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
α-helix	225-227	3
β-strand	229-230	2	10
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, B alpha chain	A, C	protein	278	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
Nucleoprotein peptide N75-83	E, F	protein	9	Human coronavirus 229E	P15130 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7LGT_1 HLA class I histocompatibility antigen, B alpha chain (chains A, C)
GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW
DRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHDQYAYDG
KDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLE
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 2 (B, D), FASTA

>7LGT_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, F), FASTA

>7LGT_3 Nucleoprotein peptide N75-83 (chains E, F)
SPKLHFYYL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	11

Water and common crystallization additives (NA, CL, K, BR) are not listed.

Primary citation

CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses. Lineburg, K.E., Grant, E.J., Swaminathan, S. et al. Immunity (2021) 54:1055. DOI 10.1016/j.immuni.2021.04.006 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide

Browse structure collections

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