7RDV: TFH TCR

TFH TCR bound to MHC Class II IAd presenting aggrecan epitope. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 6,052
Mol. weight: 94.08 kDa
Ligands: NAG
Released: 27 Jul 2022

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

Secondary structure: helices and β-sheets

7RDV contains 19 α-helices and 72 β-strands across 5 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-49	4
α-helix	56-76	21
α-helix	80-82	3
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	127-128	2	3
β-strand	132-134	3	2
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-166	6	3
β-strand	174-178	5	3

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-87	5
α-helix	88-89	2
β-strand	95	1	4
β-strand	98-103	6	5
β-strand	115-122	8	5
β-strand	123	1	4
β-strand	128-130	3	6
β-strand	142-144	3	5
β-strand	148-150	3	5
β-strand	154-161	8	5
β-strand	173	1	7
β-strand	174-176	3	6
β-strand	186	1	7

Chain C: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	30-44	9	9
β-strand	50-57	8	9
β-strand	66-69	4	8
β-strand	79-84	6	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-103	4	9
β-strand	105-106	2	10
β-strand	107-108	2	9
β-strand	115-116	2	10
β-strand	120-125	6	9
α-helix	126-127	2
β-strand	134-137	4	11
β-strand	147-152	6	11
α-helix	160-162	3
β-strand	168-170	3	11
β-strand	174-176	3	11
β-strand	185-192	8	11

Chain D: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	31-44	7	13
β-strand	51-56	6	13
β-strand	67-68	2	13
β-strand	77-79	3	14
β-strand	86	1	12
β-strand	88-91	4	14
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	114-116	3	13
β-strand	120-125	6	13
α-helix	128-130	3
β-strand	132	1	15
β-strand	135-139	5	16
α-helix	140-142	3
α-helix	143-149	7
β-strand	151-161	11	16
β-strand	162	1	15
β-strand	166-172	7	17
β-strand	175-177	3	17
β-strand	181-183	3	16
β-strand	188-189	2	16
β-strand	199-208	10	16
α-helix	209-212	4
β-strand	218-225	8	17
β-strand	228	1	18
β-strand	242	1	18
β-strand	244-251	8	17

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	94-100	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-D alpha chain	A	protein	181	Mus musculus	P04228 (AlphaFold model)
H-2 class II histocompatibility antigen, A-D beta chain	B	protein	186	Mus musculus	P01921 (AlphaFold model)
TFH TCR alpha chain	C	protein	205	Mus musculus
TFH TCR beta chain	D	protein	240	Mus musculus
Aggrecan core peptide	H	protein	12	Homo sapiens	P16112 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7RDV_1 H-2 class II histocompatibility antigen, A-D alpha chain (chains A)
EADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGL
QNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINIT
WLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWTS
G

Sequence of entity 2 (B), FASTA

>7RDV_2 H-2 class II histocompatibility antigen, A-D beta chain (chains B)
ERHFVVQFKGECYYTNGTQRIRLVTRYIYNREEYVRYDSDVGEYRAVTELGRPDAEYWNS
QPEILERTRAEVDTACRHNYEGPETSTSLRRLEQPNVAISLSRTEALNHHNTLVCSVTDF
YPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHVEHPSLKS
PITVEW

Sequence of entity 3 (C), FASTA

>7RDV_3 TFH TCR alpha chain (chains C)
EQVEQLPSILRVQEGSSASINCTYENSASNYFPWYKQEPGENPKLIIDIRSNMERKQTQG
LIVLLDKKAKRFSLHITDTQPGDSAMYFCAASDDNNNRIFFGDGTQLVVKPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>7RDV_4 TFH TCR beta chain (chains D)
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQENFSLILELATPSQTSVYFCASGGQSNERLFFGHGTKLSVLEDLNKVFPPE
VAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Sequence of entity 5 (H), FASTA

>7RDV_5 Aggrecan core peptide (chains H)
EGRVRVNSAYQS

Ligands and cofactors

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

Primary citation

TFH TCR bound to MHC Class II IAd presenting aggrecan epitope. Lim, J.J., Rossjohn, J., Reid, H. To be published.

Other PDB entries of the same protein (UniProt P04228 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BLQ 1.8 Å, Crystal Structure of IAg7 in complex with insulin mimotope p8E9E
7QHP 1.82 Å, Structure of I-Ag7 with a bound hybrid insulin peptide
6BLR 1.96 Å, Crystal Structure of IAg7 in complex with insulin mimotope p8E9E6SS
6BLX 2.32 Å, Crystal structure of IAg7 in complex with insulin mimotope p8G9E
2IAD 2.4 Å, Class II MHC I-ad in complex with an influenza hemagglutinin peptide 126-138
5DMK 2.45 Å, Crystal Structure of IAg7 in complex with RLGL-WE14
1ES0 2.6 Å, Crystal structure of the murine class II allele I-A(G7) complexed with the glutamic acid…
1IAO 2.6 Å, Class II MHC I-ad in complex with ovalbumin peptide 323-339
7Z50 2.65 Å, Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin…
3MBE 2.89 Å, TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
3CUP 3.09 Å, Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide…
1F3J 3.1 Å, Histocompatibility antigen I-AG7

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