4P46: J809.B5 Y31A TCR

J809.B5 Y31A TCR bound to IAb3K. Determined by X-ray diffraction at 2.85 Å resolution. Released 28 May 2014.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Mus musculus, Synthetic Construct
Chains: 4
Atoms: 6,273
Mol. weight: 94.3 kDa
Released: 28 May 2014

Explore 4P46 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P46 contains 24 α-helices and 73 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: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	9-13	5	9
α-helix	17	1
β-strand	18-24	7	8
β-strand	31-37	7	9
β-strand	44-50	7	9
β-strand	56-59	4	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-90	5	9
β-strand	91-92	2	10
β-strand	93	1	9
β-strand	100-101	2	10
β-strand	105-110	6	9
α-helix	111-112	2
β-strand	119-125	7	11
β-strand	132-137	6	11
α-helix	146-148	3
β-strand	153-155	3	11
β-strand	159-162	4	11
β-strand	169-177	9	11
β-strand	198	1	11

Chain B: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
β-strand	8-12	5	9
β-strand	17-23	7	12
β-strand	29-36	8	9
β-strand	40-47	8	9
β-strand	54-55	2	9
β-strand	62-65	4	12
β-strand	72-76	5	12
α-helix	81-83	3
β-strand	85-92	8	9
β-strand	100-101	2	9
β-strand	105-110	6	9
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-125	6	11
α-helix	128-134	7
β-strand	136-146	11	11
β-strand	147	1	13
β-strand	151-157	7	14
β-strand	160-162	3	14
β-strand	166-168	3	11
β-strand	173-174	2	11
β-strand	184-193	10	11
α-helix	194-197	4
β-strand	203-210	8	14
β-strand	213	1	15
β-strand	227	1	15
β-strand	229-236	8	14

Chain C: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-49	4
β-strand	53	1	2
α-helix	57-76	20
α-helix	80-84	5
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	133-134	2	3
α-helix	136-137	2
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
α-helix	173	1
β-strand	174-177	4	4

Chain D: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-24	1	2
α-helix	-23--22	2
α-helix	-18--14	5
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	48-49	2	1
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-87	5
α-helix	91-93	3
β-strand	96	1	5
β-strand	99-104	6	6
β-strand	114-123	10	6
β-strand	124	1	5
β-strand	129-134	6	7
β-strand	137-139	3	7
β-strand	143-145	3	6
α-helix	146-148	3
β-strand	149-150	2	6
β-strand	156-164	9	6
β-strand	171-177	7	7
β-strand	185-190	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-B alpha chain	C	protein	179	Mus musculus	P14434 (AlphaFold model)
3K Peptide,H-2 class II histocompatibility antigen, A beta chain	D	protein	218	Synthetic Construct, Mus musculus	P14483 (AlphaFold model)
J809.B5 TCR Y31A alpha chain (Va2.8)	A	protein	199	Mus musculus
J809.B5 TCR beta chain (Vb8.2)	B	protein	238	Mus musculus	P01850 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>4P46_1 H-2 class II histocompatibility antigen, A-B alpha chain (chains C)
IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG
LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW

Sequence of entity 2 (D), FASTA

>4P46_2 3K Peptide,H-2 class II histocompatibility antigen, A beta chain (chains D)
FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQ

Sequence of entity 3 (A), FASTA

>4P46_3 J809.B5 TCR Y31A alpha chain (Va2.8) (chains A)
QVRQSPQSLTVWEGETAILNCSYENSAFDAFPWYQQFPGEGPALLIAIRSVSDKKEDGRF
TIFFNKREKKLSLHITDSQPGDSATYFCAASKGADRLTFGKGTQLIIQPYIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPS

Sequence of entity 4 (B), FASTA

>4P46_4 J809.B5 TCR beta chain (Vb8.2) (chains B)
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR

Primary citation

Effect of CDR3 Sequences and Distal V Gene Residues in Regulating TCR-MHC Contacts and Ligand Specificity. Stadinski, B.D., Trenh, P., Duke, B. et al. J Immunol (2014) 192:6071-6082. DOI 10.4049/jimmunol.1303209 · PubMed

Other PDB entries of the same protein (UniProt P14434 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VQ8 2.01 Å, Immune receptor complex
8RAL 2.1 Å, CL3E peptide bound to the I-Ab murine MHC class II receptor
1MUJ 2.15 Å, Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide
4P23 2.25 Å, J809.B5 TCR bound to IAb/3K
1LNU 2.5 Å, Crystal structure of class II MHC molecule iab bound to EALPHA3K peptide
3C5Z 2.55 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
6MNG 2.66 Å, 4738 TCR bound to IAb Padi4
3RDT 2.7 Å, Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide
6MNN 2.83 Å, 6236 TCR bound to I-Ab Padi4
6MNO 2.9 Å, 6235 TCR bound to I-Ab Padi4
9AUD 2.9 Å, Immune receptor complex
3C60 3.05 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR YAe62

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