7N2Q: AS4.3-yeih-HLA*B27

AS4.3-yeih-HLA*B27. Determined by X-ray diffraction at 2.7 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 10
Atoms: 13,409
Mol. weight: 191.42 kDa
Ligands: NAG
Released: 7 Dec 2022

Explore 7N2Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N2Q contains 47 α-helices and 142 β-strands across 8 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.

Chains A and H: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	10
α-helix	20	1
β-strand	21-28	8	10
β-strand	31-37	7	10
β-strand	46-47	2	10
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	10
β-strand	109-118	10	10
β-strand	121-126	6	10
β-strand	133-135	3	10
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
α-helix	182	1
β-strand	183	1	11
α-helix	184-185	2
β-strand	186-193	8	12
β-strand	198-208	11	12
β-strand	209	1	11
β-strand	214-219	6	13
β-strand	222-223	2	13
β-strand	228-230	3	12
β-strand	234-235	2	12
β-strand	241-250	10	12
α-helix	254-256	3
β-strand	257-262	6	13
β-strand	270-272	3	13

Chains B and I: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	14
α-helix	4-5	2
β-strand	6-11	6	15
β-strand	21-30	10	15
β-strand	31	1	14
β-strand	35-41	7	16
β-strand	44-45	2	16
α-helix	46	1
β-strand	50-51	2	15
α-helix	52-54	3
β-strand	55-56	2	15
β-strand	62-70	9	15
β-strand	78-84	7	16
β-strand	91-94	4	16

Chain D: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
β-strand	11-15	5	2
β-strand	20-26	7	1
β-strand	33-40	8	2
β-strand	44-52	9	2
β-strand	57-60	4	1
β-strand	63-68	6	1
β-strand	73-78	6	1
α-helix	83-85	3
β-strand	88-94	7	2
β-strand	99-101	3	2
β-strand	105-110	6	2
β-strand	119-123	5	3
α-helix	124-126	3
β-strand	132-137	6	3
β-strand	153-155	3	3
α-helix	156-158	3
β-strand	159-163	5	3
β-strand	168-177	10	3
α-helix	184-187	4
β-strand	198	1	3

Chain E: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	17
β-strand	11-15	5	18
β-strand	20-26	7	17
β-strand	33-40	8	18
β-strand	44-52	9	18
β-strand	57-60	4	17
β-strand	63-68	6	17
β-strand	73-78	6	17
α-helix	83-85	3
β-strand	88-94	7	18
β-strand	99-101	3	18
β-strand	105-110	6	18
β-strand	119-122	4	19
α-helix	123-126	4
β-strand	132-137	6	19
β-strand	153-155	3	19
α-helix	156-158	3
β-strand	159-163	5	19
β-strand	168-177	10	19
β-strand	198	1	19

Chains F and G: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	4
β-strand	10-14	5	5
β-strand	19-24	6	4
β-strand	31-38	8	5
β-strand	42-50	9	5
β-strand	53-57	5	5
β-strand	64-68	5	4
β-strand	74-78	5	4
α-helix	83-85	3
β-strand	87-94	8	5
β-strand	104-105	2	5
β-strand	109-114	6	5
α-helix	117-119	3
β-strand	121	1	6
β-strand	124-128	5	7
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	7
β-strand	151	1	6
β-strand	155-161	7	8
β-strand	164-166	3	8
β-strand	170-172	3	7
α-helix	176	1
β-strand	177-178	2	7
β-strand	188-197	10	7
α-helix	198-202	5
β-strand	207-214	8	8
β-strand	217	1	9
α-helix	228-229	2
β-strand	231	1	9
β-strand	233-240	8	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AS4.3 T cell receptor alpha chain	D, E	protein	204	Homo sapiens
AS4.3 T cell receptor beta chain	F, G	protein	241	Homo sapiens
Human leukocyte antigen B27	A, H	protein	278	Homo sapiens	A3F718 (AlphaFold model)
Beta-2-microglobulin	B, I	protein	100	Homo sapiens	P61769 (AlphaFold model)
YeiH protein	C, J	protein	9	Escherichia coli	P62723 (AlphaFold model)

Sequence of entity 1 (D, E), FASTA

>7N2Q_1 AS4.3 T cell receptor alpha chain (chains D, E)
KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSG
RLNASLDKSSGRSTLYIAASQPGDSATYLCAVSNFNKFYFGSGTKLNVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (F, G), FASTA

>7N2Q_2 AS4.3 T cell receptor beta chain (chains F, G)
VTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILER
FSAQQFPDLHSELNLSSLELGDSALYFCASSVATYSTDTQYFGPGTRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Sequence of entity 3 (A, H), FASTA

>7N2Q_3 Human leukocyte antigen B27 (chains A, H)
GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW
DRETQISKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 4 (B, I), FASTA

>7N2Q_4 Beta-2-microglobulin (chains B, I)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (C, J), FASTA

>7N2Q_5 YeiH protein (chains C, J)
LRVMMLAPF

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Water and common crystallization additives (SO4, 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 A3F718 (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
9PBH 2.13 Å, AS19.2 TCR complex with PSG5-HLA B*27:05
8CX4 2.2 Å, TCR-antigen complex AS8.4-YEIH-HLA*B27
7N2R 2.28 Å, AS4.3-PRPF3-HLA*B27
7N2O 2.3 Å, AS4.2-yeih-HLA*B27
7N2S 2.37 Å, AS3.1-PRPF3-HLA*B27
7N2P 2.5 Å, AS4.3-RNASEH2b-HLA*B27
7N2N 2.6 Å, TCR-antigen complex AS4.2-PRPF3-HLA*B27
7T0L 3.0 Å, HLA-B*27:05 in complex with the pan-HLA-Ia monoclonal antibody W6/32

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