4P23: J809.B5 TCR

J809.B5 TCR bound to IAb/3K. Determined by X-ray diffraction at 2.25 Å resolution. Released 28 May 2014.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,736
Mol. weight: 94.41 kDa
Released: 28 May 2014

Explore 4P23 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P23 contains 28 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	9-13	5	2
α-helix	17	1
β-strand	18-24	7	1
β-strand	31-37	7	2
β-strand	44-50	7	2
β-strand	56-59	4	1
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-90	5	2
β-strand	91-92	2	3
β-strand	93	1	2
β-strand	100-101	2	3
β-strand	105-110	6	2
α-helix	111-112	2
β-strand	119-125	7	4
β-strand	132-137	6	4
α-helix	146-148	3
β-strand	153-155	3	4
α-helix	156-158	3
β-strand	159-163	5	4
α-helix	164-166	3
β-strand	168-177	10	4
α-helix	184-186	3
β-strand	198	1	4

Chain B: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	5
β-strand	8-12	5	6
β-strand	17-23	7	5
β-strand	29-36	8	6
β-strand	40-49	10	6
β-strand	52-55	4	6
β-strand	63-65	3	5
β-strand	71-76	6	5
α-helix	81-83	3
β-strand	85-92	8	6
β-strand	100-101	2	6
β-strand	105-110	6	6
α-helix	113-115	3
β-strand	117	1	7
α-helix	118-119	2
β-strand	120-125	6	4
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	4
β-strand	147	1	7
β-strand	151-157	7	8
β-strand	160-162	3	8
β-strand	166-168	3	4
β-strand	173-174	2	4
β-strand	184-193	10	4
α-helix	194-198	5
β-strand	203-210	8	8
β-strand	213	1	9
α-helix	224-225	2
β-strand	227	1	9
β-strand	229-236	8	8

Chain C: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	10
β-strand	19-26	8	10
β-strand	29-35	7	10
β-strand	40-43	4	10
α-helix	46-51	6
β-strand	53	1	11
α-helix	56-76	21
α-helix	80-84	5
β-strand	88-93	6	12
β-strand	103-112	10	12
β-strand	118-123	6	13
β-strand	126-128	3	13
β-strand	133-134	2	12
α-helix	137	1
β-strand	138-139	2	12
β-strand	145-153	9	12
β-strand	161-166	6	13
β-strand	174-177	4	13

Chain D: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-24	1	11
α-helix	-18--14	5
β-strand	7-18	12	10
β-strand	23-32	10	10
β-strand	35-41	7	10
β-strand	46-49	4	10
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-87	5
α-helix	91-93	3
β-strand	96	1	14
α-helix	97-98	2
β-strand	99-104	6	15
β-strand	114-123	10	15
β-strand	124	1	14
β-strand	129-134	6	16
β-strand	137-139	3	16
β-strand	143-145	3	15
α-helix	146-148	3
β-strand	149-150	2	15
β-strand	156-164	9	15
β-strand	171-177	7	16
β-strand	185-190	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
J809.B5 TCR V alpha chain (Va2.8)	A	protein	199	Mus musculus
J809.B5 TCR V beta chain (Vb8.2)	B	protein	239	Mus musculus
H-2 class II histocompatibility antigen, A-B alpha chain	C	protein	179	Mus musculus	P14434 (AlphaFold model)
3K peptide and MHC IAb beta chain,H-2 class II histocompatibility antigen, A beta chain	D	protein	218	Mus musculus	P14483 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4P23_1 J809.B5 TCR V alpha chain (Va2.8) (chains A)
QVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLIAIRSVSDKKEDGRF
TIFFNKREKKLSLHITDSQPGDSATYFCAASKGADRLTFGKGTQLIIQPYIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSETNVSESKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKAAF
ACANAFNNSIIPEDTFFPS

Sequence of entity 2 (B), FASTA

>4P23_2 J809.B5 TCR V beta chain (Vb8.2) (chains B)
AVTQSPRNKVAVTGGKVTLSCDQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQEDFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA

Sequence of entity 3 (C), FASTA

>4P23_3 H-2 class II histocompatibility antigen, A-B alpha chain (chains C)
IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG
LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW

Sequence of entity 4 (D), FASTA

>4P23_4 3K peptide and MHC IAb beta chain,H-2 class II histocompatibility antigen, A beta chain (chains D)
FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTDGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQ

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
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
4P46 2.85 Å, J809.B5 Y31A TCR bound to IAb3K
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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