7NME: MHC class I antigen

Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR. Determined by X-ray diffraction at 2.2 Å resolution. Released 7 Sept 2022.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,814
Mol. weight: 94.08 kDa
Ligands: BTB
Released: 7 Sept 2022

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

Secondary structure: helices and β-sheets

7NME contains 28 α-helices and 75 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: 11 helices, 19 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
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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
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	223	1	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

Chain B: 4 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
α-helix	90	1
β-strand	91-94	4	7

Chain D: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	8
β-strand	10-14	5	9
α-helix	18	1
β-strand	19-24	6	8
β-strand	32-38	7	9
β-strand	45-51	7	9
β-strand	56-59	4	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	99-102	4	9
β-strand	106-111	6	9
α-helix	112	1
β-strand	119-124	6	10
β-strand	125	1	11
β-strand	132-139	8	10
β-strand	143-145	3	12
α-helix	146-148	3
β-strand	153-155	3	10
α-helix	156-158	3
β-strand	159-163	5	10
β-strand	168-177	10	10
α-helix	184-186	3
β-strand	190-192	3	12

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	13
β-strand	11-15	5	14
β-strand	20-25	6	13
β-strand	32-38	7	14
β-strand	45-51	7	14
β-strand	54-58	5	14
β-strand	66-69	4	13
β-strand	71	1	15
β-strand	73	1	15
β-strand	76-80	5	13
α-helix	85-87	3
β-strand	89-96	8	14
α-helix	100-101	2
β-strand	102-103	2	14
β-strand	107-112	6	14
α-helix	115-117	3
β-strand	119	1	16
α-helix	120-121	2
β-strand	122-126	5	11
α-helix	127-129	3
α-helix	130-136	7
β-strand	138-148	11	11
β-strand	149	1	16
β-strand	153-159	7	17
β-strand	162-163	2	17
β-strand	168-170	3	11
β-strand	175-176	2	11
β-strand	186-195	10	11
α-helix	196-199	4
β-strand	205-212	8	17
β-strand	215	1	18
β-strand	229	1	18
β-strand	231-238	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	A0A5H2UYS3 (AlphaFold model)
Human MHC Class I, beta 2 microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Gln-leu-pro-arg-leu-phe-pro-leu-leu	C	protein	9	Homo sapiens
4C6 Human T-cell Receptor, alpha Chain	D	protein	192	Homo sapiens
4C6 Human T-cell Receptor, beta Chain	E	protein	240	Homo sapiens

Sequence of entity 1 (A), FASTA

>7NME_1 MHC class I antigen (chains A)
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>7NME_2 Human MHC Class I, beta 2 microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7NME_3 GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU (chains C)
QLPRLFPLL

Sequence of entity 4 (D), FASTA

>7NME_4 4C6 Human T-cell Receptor, alpha Chain (chains D)
GEDVEQSLFLSVREGDSSVINCTYTDSSSTYLYWYKQEPGAGLQLLTYIFSNMDMKQDQR
LTVLLNKKDKHLSLRIADTQTGDSAIYFCAEPSGNTGKLIFGQGTTLQVKPIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSII

Sequence of entity 5 (E), FASTA

>7NME_5 4C6 Human T-cell Receptor, beta Chain (chains E)
TGVSQDPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSRLL
SDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLHHEQYFGPGTRLTVTEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
BTB	2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol	C8 H19 N O5	1

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR. Rizkallahp, P.J., Sewell, A.K., Cole, D.K. et al. To be published.

Other PDB entries of the same protein (UniProt A0A5H2UYS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7JYV 1.51 Å, Crystal Structure of HLA A*2402 in complex with YFSPIRVTF, an 9-mer influenza epitope
7MJA 1.69 Å, HLA-A*24:02 bound to Neuroblastoma derived PHOX2B peptide
7EJM 1.71 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
8SBK 1.8 Å, Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI (ATG2A).
7WT3 1.89 Å, Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide
7EJL 1.89 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein
7WT4 1.89 Å, Crystal structure of HLA-A*2402 complexed with 8-mer Influenza PB1 peptide
7K81 2.0 Å, KIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide
7EJN 2.11 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-HKU1) spike protein
6XQA 2.16 Å, Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from…
7NMD 2.25 Å, Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL
7K80 2.4 Å, KIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide

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