7N2R: AS4.3-PRPF3-HLA*B27

AS4.3-PRPF3-HLA*B27. Determined by X-ray diffraction at 2.28 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,612
Mol. weight: 96.3 kDa
Ligands: NAG, ASP
Released: 7 Dec 2022

Explore 7N2R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N2R contains 20 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	11
α-helix	20	1
β-strand	21-28	8	11
β-strand	31-37	7	11
β-strand	46-47	2	11
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	11
β-strand	109-118	10	11
β-strand	121-126	6	11
β-strand	133-135	3	11
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	12
α-helix	184-185	2
β-strand	188-192	5	13
β-strand	200-208	9	13
β-strand	209	1	12
β-strand	214	1	14
β-strand	229-230	2	13
α-helix	231-233	3
β-strand	234-235	2	13
β-strand	241-247	7	13
β-strand	259-261	3	15
β-strand	262	1	14
β-strand	270-272	3	15

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	16
β-strand	6-11	6	17
β-strand	21-30	10	17
β-strand	31	1	16
β-strand	36-41	6	18
β-strand	44-45	2	18
α-helix	46	1
β-strand	50-51	2	17
β-strand	55-56	2	17
β-strand	62-70	9	17
β-strand	78-83	6	18
β-strand	91-94	4	18

Chain D: 3 helices, 19 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	87-95	9	2
β-strand	98-101	4	2
β-strand	105-110	6	2
β-strand	119-123	5	3
β-strand	124	1	4
α-helix	125	1
β-strand	133-137	5	3
β-strand	153-155	3	3
α-helix	156-158	3
β-strand	161-163	3	5
β-strand	168-170	3	5
β-strand	172-177	6	3
β-strand	198	1	3

Chain F: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	9-13	5	2
β-strand	18-23	6	6
β-strand	30-37	8	2
β-strand	41-49	9	2
β-strand	52-56	5	2
β-strand	63-67	5	6
β-strand	73-77	5	6
α-helix	82-84	3
β-strand	86-93	8	2
β-strand	103-104	2	2
β-strand	108-113	6	2
α-helix	116-118	3
β-strand	120	1	7
β-strand	123-127	5	8
β-strand	128	1	4
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	8
β-strand	150	1	7
β-strand	154-160	7	9
β-strand	163-165	3	9
β-strand	169-171	3	8
β-strand	176-177	2	8
β-strand	187-196	10	8
α-helix	197-201	5
β-strand	206-213	8	9
β-strand	216	1	10
α-helix	227-228	2
β-strand	230	1	10
β-strand	232-239	8	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AS4.3 T cell receptor alpha chain	D	protein	204	Homo sapiens
AS4.3 T cell receptor beta chain	F	protein	242	Homo sapiens
Human leukocyte antigen (HLA) B27	A	protein	278	Homo sapiens	A3F718 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Pre-MRNA Processing Factor 3	C	protein	9	Homo sapiens	O43395 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>7N2R_1 AS4.3 T cell receptor alpha chain (chains D)
KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSG
RLNASLDKSSGRSTLYIAASQPGDSATYLCAVSNFNKFYFGSGTKLNVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (F), FASTA

>7N2R_2 AS4.3 T cell receptor beta chain (chains F)
GVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILE
RFSAQQFPDLHSELNLSSLELGDSALYFCASSVATYSTDTQYFGPGTRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Sequence of entity 3 (A), FASTA

>7N2R_3 Human leukocyte antigen (HLA) B27 (chains A)
GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW
DRETQISKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 4 (B), FASTA

>7N2R_4 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (C), FASTA

>7N2R_5 Pre-MRNA Processing Factor 3 (chains C)
TRLALIAPK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
ASP	Aspartic acid	C4 H7 N O4	1

Water and common crystallization additives (EDO, 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
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
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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