7N2P: AS4.3-RNASEH2b-HLA*B27

AS4.3-RNASEH2b-HLA*B27. Determined by X-ray diffraction at 2.5 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,623
Mol. weight: 96.17 kDa
Ligands: NAG
Released: 7 Dec 2022

Explore 7N2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N2P contains 25 α-helices and 71 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	57-85	29
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	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	3
β-strand	200-208	9	3
β-strand	209	1	2
β-strand	214	1	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-248	8	3
β-strand	259-260	2	5
β-strand	262	1	4
β-strand	271-272	2	5

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Chain D: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	9
β-strand	11-15	5	10
β-strand	20-26	7	9
β-strand	33-40	8	10
β-strand	44-52	9	10
β-strand	57-60	4	9
β-strand	63-68	6	9
β-strand	73-78	6	9
α-helix	83-85	3
β-strand	88-94	7	10
β-strand	99-101	3	10
β-strand	105-110	6	10
α-helix	111-112	2
β-strand	119-122	4	11
α-helix	123-124	2
β-strand	133-137	5	11
α-helix	146-148	3
β-strand	154-155	2	11
α-helix	156-158	3
β-strand	159-163	5	11
α-helix	164-166	3
β-strand	168-176	9	11
β-strand	198	1	11

Chain F: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
α-helix	25-26	2
β-strand	31-38	8	13
β-strand	42-50	9	13
β-strand	53-57	5	13
β-strand	64-68	5	12
β-strand	74-78	5	12
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	104-105	2	13
β-strand	109-114	6	13
α-helix	117-119	3
β-strand	121	1	14
β-strand	124-128	5	15
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	15
β-strand	151	1	14
β-strand	155-161	7	16
β-strand	165-166	2	16
β-strand	170-172	3	15
β-strand	177-178	2	15
β-strand	188-197	10	15
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
Human leukocyte antigen (HLA) B27	A	protein	278	Homo sapiens	A3F718 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Ribonuclease H2 subunit B	C	protein	9	Homo sapiens	A0A2R8Y7R8 (AlphaFold model)
AS4.3 T cell receptor alpha chain	D	protein	204	Homo sapiens
AS4.3 T cell receptor beta chain	F	protein	242	Homo sapiens

Sequence of entity 1 (A), FASTA

>7N2P_1 Human leukocyte antigen (HLA) B27 (chains A)
GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW
DRETQISKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 2 (B), FASTA

>7N2P_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7N2P_3 Ribonuclease H2 subunit B (chains C)
GQVMVVAPR

Sequence of entity 4 (D), FASTA

>7N2P_4 AS4.3 T cell receptor alpha chain (chains D)
KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSG
RLNASLDKSSGRSTLYIAASQPGDSATYLCAVSNFNKFYFGSGTKLNVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (F), FASTA

>7N2P_5 AS4.3 T cell receptor beta chain (chains F)
GVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILE
RFSAQQFPDLHSELNLSSLELGDSALYFCASSVATYSTDTQYFGPGTRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (GOL, SO4) 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
7N2N 2.6 Å, TCR-antigen complex AS4.2-PRPF3-HLA*B27
7N2Q 2.7 Å, AS4.3-yeih-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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