7N2O: AS4.2-yeih-HLA*B27

AS4.2-yeih-HLA*B27. Determined by X-ray diffraction at 2.3 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,738
Mol. weight: 96.07 kDa
Ligands: NAG
Released: 7 Dec 2022

Explore 7N2O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N2O contains 23 α-helices and 74 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: 10 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	138-149	12
α-helix	152-161	10
α-helix	163-174	12
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	213-219	7	4
β-strand	222-223	2	4
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	257-263	7	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	35-41	7	7
β-strand	44-45	2	7
α-helix	46-47	2
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	78-84	7	7
β-strand	91-94	4	7
α-helix	95-96	2

Chain D: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	8
β-strand	11-15	5	9
β-strand	20-26	7	8
β-strand	33-39	7	9
β-strand	45-52	8	9
β-strand	57-60	4	8
β-strand	63-66	4	8
β-strand	68	1	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	87-96	10	9
β-strand	103-107	5	9
β-strand	111-116	6	9
α-helix	117-119	3
β-strand	125-129	5	10
β-strand	130-131	2	11
β-strand	139-143	5	10
β-strand	160-161	2	10
β-strand	166-169	4	12
β-strand	174-177	4	12
β-strand	178-182	5	10
β-strand	204	1	10

Chain F: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	19-24	6	13
α-helix	25-26	2
β-strand	31-38	8	14
β-strand	42-50	9	14
β-strand	53-57	5	14
β-strand	64-68	5	13
β-strand	74-78	5	13
α-helix	83-85	3
β-strand	87-94	8	14
β-strand	104-105	2	14
β-strand	109-114	6	14
α-helix	117-119	3
β-strand	121	1	15
β-strand	124-129	6	11
α-helix	130-131	2
α-helix	132-137	6
β-strand	140-150	11	11
β-strand	151	1	15
β-strand	155-161	7	16
β-strand	164-166	3	16
β-strand	170-172	3	11
β-strand	177-178	2	11
β-strand	188-197	10	11
α-helix	198-202	5
β-strand	207-214	8	16
β-strand	217	1	17
α-helix	228-229	2
β-strand	231	1	17
β-strand	233-240	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
YeiH protein	C	protein	9	Homo sapiens	P62723 (AlphaFold model)
Human leukocyte antigen (HLA) B27	A	protein	278	Homo sapiens	A3F718 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
T-cell receptor alpha chain	D	protein	210	Homo sapiens
T-cell receptor beta chain	F	protein	242	Homo sapiens

Sequence of entity 1 (C), FASTA

>7N2O_1 YeiH protein (chains C)
LRVMMLAPF

Sequence of entity 2 (A), FASTA

>7N2O_2 Human leukocyte antigen (HLA) B27 (chains A)
GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW
DRETQISKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 3 (B), FASTA

>7N2O_3 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 4 (D), FASTA

>7N2O_4 T-cell receptor alpha chain (chains D)
KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSG
RLNASLDKSSGRSTLYIAASQPGDSATYLCAVLSPVQETSGSRLTFGEGTQLTVNPDIQN
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
WSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (F), FASTA

>7N2O_5 T-cell receptor beta chain (chains F)
GVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILE
RFSAQQFPDLHSELNLSSLELGDSALYFCASSVGLFSTDTQYFGPGTRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (GOL) are not listed.

Primary citation

Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Yang, X., Garner, L.I., Zvyagin, I.V. et al. Nature (2022) 612:771-777. DOI 10.1038/s41586-022-05501-7 · PubMed

Other PDB entries of the same protein (UniProt P62723 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PBG 2.0 Å, TCR 19.2 complex with YEIH-HLA B*27:05
8CX4 2.2 Å, TCR-antigen complex AS8.4-YEIH-HLA*B27
7N2Q 2.7 Å, AS4.3-yeih-HLA*B27

Browse structure collections

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