6MKD: 4699 TCR

4699 TCR bound to I-Ab Padi4. Determined by X-ray diffraction at 3.2 Å resolution. Released 3 Jul 2019.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Mus musculus
Chains: 4
Atoms: 5,916
Mol. weight: 95.26 kDa
Released: 3 Jul 2019

Explore 6MKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MKD contains 24 α-helices and 76 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	3-4	2	9
β-strand	9-13	5	10
β-strand	18-24	7	9
β-strand	31-37	7	10
β-strand	44-50	7	10
β-strand	56-59	4	9
β-strand	62-67	6	9
β-strand	72-77	6	9
α-helix	82-84	3
β-strand	87-90	4	10
β-strand	91-92	2	11
β-strand	93	1	10
α-helix	95-97	3
β-strand	103-104	2	11
β-strand	108-113	6	10
β-strand	122-126	5	12
β-strand	127	1	13
β-strand	136-140	5	12
α-helix	158-161	4
β-strand	162-165	4	12
β-strand	172-178	7	12
α-helix	187-190	4
β-strand	201	1	12

Chain B: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	14
β-strand	8-12	5	15
β-strand	17	1	16
β-strand	20-23	4	14
β-strand	29-36	8	15
β-strand	40-47	8	15
β-strand	54-55	2	15
β-strand	62-65	4	16
β-strand	71-72	2	14
β-strand	73-76	4	16
α-helix	81-83	3
β-strand	85-92	8	15
β-strand	100-101	2	15
β-strand	105-110	6	15
α-helix	113-115	3
β-strand	117	1	17
α-helix	118-119	2
β-strand	120-124	5	18
β-strand	125	1	13
α-helix	126-127	2
α-helix	128-131	4
β-strand	136-146	11	18
β-strand	147	1	17
β-strand	151-157	7	19
β-strand	160	1	19
β-strand	166-168	3	18
β-strand	173-174	2	18
β-strand	184-193	10	18
α-helix	194-197	4
β-strand	203-210	8	19
β-strand	213	1	20
β-strand	227	1	20
β-strand	229-236	8	19

Chain C: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	1
β-strand	19-26	8	1
β-strand	30-35	6	1
β-strand	40-43	4	1
α-helix	46-51	6
β-strand	53	1	2
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	3
β-strand	88-93	6	4
β-strand	105-112	8	4
β-strand	113	1	3
β-strand	118-119	2	5
β-strand	133-134	2	4
α-helix	135-137	3
β-strand	138-139	2	4
β-strand	145-150	6	4
β-strand	164-166	3	5
β-strand	174-175	2	5

Chain D: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	-24	1	2
α-helix	-22--20	3
α-helix	-17--15	3
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	54-61	8
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	6
α-helix	97-98	2
β-strand	99-104	6	7
α-helix	107-108	2
β-strand	114-121	8	7
β-strand	124	1	6
β-strand	129-134	6	8
β-strand	138-139	2	8
β-strand	143-145	3	7
β-strand	157-164	8	7
β-strand	171-177	7	8
β-strand	185-190	6	8

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)
Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A…	D	protein	217	Mus musculus	P14483 (AlphaFold model), Q9Z183 (AlphaFold model)
4699 TCR alpha chain	A	protein	208	Mus musculus
4699 TCR beta chain	B	protein	239	Mus musculus

Sequence of entity 1 (C), FASTA

>6MKD_1 H-2 class II histocompatibility antigen, A-B alpha chain (chains C)
IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG
LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW

Sequence of entity 2 (D), FASTA

>6MKD_2 Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain (chains D)
RVSYYGPKTSPVQGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA

Sequence of entity 3 (A), FASTA

>6MKD_3 4699 TCR alpha chain (chains A)
MQQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLIAIRSVSDKKEDG
RFTIFFNKREKKLSLHITDSQPGDSATYFCAASDTGANTGKLTFGHGTILRVHPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (B), FASTA

>6MKD_4 4699 TCR beta chain (chains B)
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA

Primary citation

A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+Tregcell development. Stadinski, B.D., Blevins, S.J., Spidale, N.A. et al. Nat Immunol (2019) 20:1046-1058. DOI 10.1038/s41590-019-0414-1 · 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
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

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