7N2N: TCR-antigen complex AS4.2-PRPF3-HLA*B27

TCR-antigen complex AS4.2-PRPF3-HLA*B27. Determined by X-ray diffraction at 2.6 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,700
Mol. weight: 96.26 kDa
Ligands: NAG
Released: 7 Dec 2022

Explore 7N2N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N2N contains 27 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	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	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	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
β-strand	91-94	4	7
α-helix	95-96	2

Chain D: 5 helices, 17 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	63-68	6	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	88-95	8	9
β-strand	104-107	4	9
β-strand	111-116	6	9
α-helix	117-119	3
β-strand	125-128	4	10
β-strand	140-145	6	10
α-helix	151-154	4
β-strand	160-161	2	10
α-helix	162-164	3
β-strand	165-169	5	10
α-helix	170-172	3
β-strand	174-182	9	10
β-strand	204	1	10

Chain F: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
β-strand	31-38	8	12
β-strand	42-50	9	12
β-strand	53-57	5	12
β-strand	64-68	5	11
β-strand	74-78	5	11
α-helix	83-85	3
β-strand	87-94	8	12
β-strand	104-105	2	12
β-strand	109-114	6	12
α-helix	117-119	3
β-strand	121	1	13
α-helix	122-123	2
β-strand	124-128	5	14
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	14
β-strand	151	1	13
β-strand	155-161	7	15
β-strand	164-166	3	15
β-strand	170-172	3	14
β-strand	177-178	2	14
α-helix	186-187	2
β-strand	188-197	10	14
α-helix	198-202	5
β-strand	208-214	7	15
β-strand	217	1	12
α-helix	228-229	2
β-strand	231	1	12
β-strand	233-239	7	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pre-MRNA Processing Factor 3	C	protein	9	Homo sapiens	O43395 (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

>7N2N_1 Pre-MRNA Processing Factor 3 (chains C)
TRLALIAPK

Sequence of entity 2 (A), FASTA

>7N2N_2 Human leukocyte antigen (HLA) B27 (chains A)
GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYW
DRETQISKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 3 (B), FASTA

>7N2N_3 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 4 (D), FASTA

>7N2N_4 T cell receptor alpha chain (chains D)
KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSG
RLNASLDKSSGRSTLYIAASQPGDSATYLCAVLSPVQETSGSRLTFGEGTQLTVNPDIQN
PDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVA
WSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (F), FASTA

>7N2N_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 (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 O43395 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7N2R 2.28 Å, AS4.3-PRPF3-HLA*B27
7N2S 2.37 Å, AS3.1-PRPF3-HLA*B27
8H6L 2.6 Å, Cryo-EM structure of human exon-defined spliceosome in the early B state.
8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
6QW6 2.92 Å, Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
8Q7N 3.1 Å, cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region)
8QOZ 3.1 Å, Cryo-EM Structure of Pre-B+5'ss+ATPgammaS Complex (core part)
8QPE 3.1 Å, Cryo-EM Structure of Pre-B-like Complex (core part)
8H6E 3.2 Å, Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.
8H6J 3.25 Å, Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state.
6QX9 3.28 Å, Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
8Y6O 3.38 Å, Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11…

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