3RDT: 809.B5 TCR

Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide. Determined by X-ray diffraction at 2.7 Å resolution. Released 7 Dec 2011.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Mus musculus, synthetic construct
Chains: 4
Atoms: 6,399
Mol. weight: 95.6 kDa
Released: 7 Dec 2011

Explore 3RDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RDT contains 23 α-helices and 75 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: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	9-13	5	9
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	111-113	3
β-strand	119-125	7	11
β-strand	132-137	6	11
β-strand	153-155	3	11
β-strand	159-163	5	11
β-strand	168-177	10	11
β-strand	198	1	11

Chain B: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
β-strand	8-12	5	9
β-strand	17-19	3	13
β-strand	20-23	4	12
β-strand	29-36	8	9
β-strand	40-47	8	9
β-strand	54-55	2	9
β-strand	63-65	3	13
β-strand	71	1	12
β-strand	73-76	4	13
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	14
α-helix	118-119	2
β-strand	120-125	6	11
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	11
β-strand	147	1	14
β-strand	151-157	7	15
β-strand	160-162	3	15
β-strand	166-168	3	11
α-helix	172	1
β-strand	173-174	2	11
β-strand	184-193	10	11
α-helix	194-197	4
β-strand	203-210	8	15
β-strand	213	1	16
β-strand	227	1	16
β-strand	229-236	8	15

Chain C: 3 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	56-76	21
α-helix	81-84	4
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
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-177	4	4

Chain D: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-24	1	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	47-49	3	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	81-84	4
α-helix	87-89	3
α-helix	91-93	3
β-strand	96	1	5
α-helix	97-98	2
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	137-138	2	7
β-strand	143-145	3	6
α-helix	146-148	3
β-strand	149-150	2	6
β-strand	156-164	9	6
α-helix	166-167	2
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	182	Mus musculus	P14434 (AlphaFold model)
3K peptide, linker and MHC H-2 class II I-Ab beta chain	D	protein	217	synthetic construct, Mus musculus	P14483 (AlphaFold model)
TCR 809.B5 alpha chain	A	protein	205	Mus musculus
TCR 809.B5 beta chain	B	protein	241	Mus musculus

Sequence of entity 1 (C), FASTA

>3RDT_1 H-2 class II histocompatibility antigen, A-B alpha chain (chains C)
IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG
LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE
PE

Sequence of entity 2 (D), FASTA

>3RDT_2 3K peptide, linker and MHC H-2 class II I-Ab beta chain (chains D)
FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA

Sequence of entity 3 (A), FASTA

>3RDT_3 TCR 809.B5 alpha chain (chains A)
MQQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLIAIRSVSDKKEDG
RFTIFFNKREKKLSLHITDSQPGDSATYFCAASKGADRLTFGKGTQLIIQPYIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (B), FASTA

>3RDT_4 TCR 809.B5 beta chain (chains B)
MAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIP
DGYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Primary citation

A role for differential variable gene pairing in creating T cell receptors specific for unique major histocompatibility ligands. Stadinski, B.D., Trenh, P., Smith, R.L. et al. Immunity (2011) 35:694-704. DOI 10.1016/j.immuni.2011.10.012 · 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
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

Browse structure collections

About this viewer

MolViewer shows 3RDT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.