3C6L: Mouse MHC class II I-Ab/3K peptide

Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20. Determined by X-ray diffraction at 3.4 Å resolution. Released 29 Apr 2008.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Mus musculus
Chains: 8
Atoms: 12,716
Mol. weight: 186.08 kDa
Ligands: CA
Released: 29 Apr 2008

Explore 3C6L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C6L contains 32 α-helices and 155 β-strands across 8 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: 1 helix, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-13	5	2
β-strand	18-23	6	1
β-strand	31	1	3
β-strand	32-37	6	2
β-strand	44-49	6	2
β-strand	59	1	1
β-strand	61-66	6	1
β-strand	71-76	6	1
β-strand	86-89	4	2
β-strand	90-92	3	3
β-strand	99-101	3	3
β-strand	105-110	6	2
β-strand	119-122	4	4
β-strand	124	1	5
β-strand	134-137	4	4
β-strand	153-155	3	4
α-helix	156-158	3
β-strand	173-177	5	4

Chain B: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	6
β-strand	8-12	5	7
β-strand	17-18	2	8
β-strand	21-22	2	6
β-strand	29-35	7	7
β-strand	36	1	9
β-strand	40	1	9
β-strand	43-47	5	7
β-strand	54-55	2	7
β-strand	62	1	8
β-strand	65-68	4	6
β-strand	71-73	3	6
β-strand	75-76	2	8
α-helix	81-83	3
β-strand	85-92	8	7
β-strand	100	1	7
β-strand	106-110	5	7
α-helix	123	1
β-strand	124	1	10
β-strand	125	1	5
α-helix	128-133	6
β-strand	136-139	4	11
β-strand	140	1	10
β-strand	142-146	5	12
β-strand	151-157	7	13
β-strand	160-161	2	13
β-strand	166	1	11
β-strand	180-183	4	12
β-strand	186-189	4	11
α-helix	190-193	4
β-strand	199-206	8	13
β-strand	209	1	14
β-strand	223	1	14
β-strand	225-228	4	13
β-strand	231-232	2	13

Chain C: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	15
β-strand	20-27	8	15
β-strand	30-36	7	15
β-strand	41-44	4	15
α-helix	47-49	3
β-strand	54	1	16
α-helix	58-76	19
β-strand	89-94	6	17
β-strand	104-113	10	17
β-strand	118-124	7	18
β-strand	127-129	3	18
β-strand	133-135	3	17
α-helix	136-138	3
β-strand	139-141	3	17
β-strand	145-154	10	17
β-strand	162-168	7	18
β-strand	177-179	3	18

Chain D: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	16
α-helix	8-11	4
β-strand	34-41	8	15
β-strand	44	1	19
β-strand	49	1	19
β-strand	52-58	7	15
β-strand	61-67	7	15
β-strand	73-75	3	15
α-helix	78-80	3
α-helix	81-89	9
α-helix	91-97	7
α-helix	100	1
α-helix	101-106	6
α-helix	107-110	4
α-helix	113-115	3
β-strand	125-130	6	20
β-strand	142-149	8	20
β-strand	156-159	4	21
β-strand	164	1	21
β-strand	171-172	2	22
β-strand	175-176	2	20
β-strand	182-185	4	20
β-strand	194	1	23
β-strand	196	1	23
β-strand	198-202	5	21
β-strand	212-215	4	21

Chain E: 1 helix, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	24
β-strand	9-13	5	25
β-strand	18-23	6	24
β-strand	31	1	26
β-strand	32-37	6	25
β-strand	44-49	6	25
β-strand	59	1	24
β-strand	61-66	6	24
β-strand	71-76	6	24
α-helix	81-83	3
β-strand	86-89	4	25
β-strand	90-92	3	26
β-strand	99-101	3	26
β-strand	105-110	6	25
β-strand	119-122	4	27
β-strand	124	1	28
β-strand	134-137	4	27
β-strand	153-155	3	27
β-strand	174-177	4	27

Chain F: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	29
β-strand	8-12	5	30
β-strand	17-18	2	31
β-strand	21-22	2	29
β-strand	29-35	7	30
β-strand	36	1	32
β-strand	40	1	32
β-strand	43-47	5	30
β-strand	54-55	2	30
β-strand	62	1	31
β-strand	65-68	4	29
β-strand	71-73	3	29
β-strand	75-76	2	31
α-helix	81-83	3
β-strand	85-92	8	30
β-strand	100	1	30
β-strand	106-110	5	30
β-strand	122-124	3	33
β-strand	125	1	28
α-helix	128-133	6
β-strand	136-146	11	33
β-strand	152-157	6	34
β-strand	161-162	2	34
β-strand	166-168	3	33
α-helix	172	1
β-strand	173	1	33
α-helix	174	1
β-strand	180-189	10	33
α-helix	190-193	4
β-strand	199-206	8	34
β-strand	225-232	8	34

Chain G: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-15	10	35
β-strand	20-27	8	35
β-strand	30-35	6	35
β-strand	42-43	2	35
α-helix	47-50	4
β-strand	54	1	36
α-helix	58-77	20
β-strand	86	1	37
β-strand	89-94	6	38
β-strand	104-113	10	38
β-strand	114	1	37
β-strand	119-124	6	39
β-strand	127-128	2	39
α-helix	129	1
β-strand	135	1	38
β-strand	139-140	2	38
β-strand	146-154	9	38
β-strand	162-167	6	39
α-helix	176	1
β-strand	177-179	3	39

Chain H: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	36
β-strand	34-44	11	35
β-strand	49-58	10	35
β-strand	61-67	7	35
β-strand	73-75	3	35
α-helix	78-80	3
α-helix	81-89	9
α-helix	91-100	10
α-helix	101-106	6
α-helix	107-110	4
α-helix	113-115	3
β-strand	127-130	4	40
β-strand	142-149	8	40
β-strand	156-159	4	41
β-strand	164	1	41
β-strand	170-171	2	22
β-strand	175-176	2	40
β-strand	182-188	7	40
β-strand	198-202	5	41
β-strand	211-215	5	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR 2W20 alpha chain	A, E	protein	185	Mus musculus	P01849 (AlphaFold model)
TCR 2W20 beta chain	B, F	protein	236	Mus musculus	P01852 (AlphaFold model)
H-2 class II histocompatibility antigen, A-B alpha chain	C, G	protein	182	Mus musculus	P14434 (AlphaFold model)
3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain)	D, H	protein	217	Mus musculus	P14483 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>3C6L_1 TCR 2W20 alpha chain (chains A, E)
QQVRQSPQSLTVWEGETAILNCSYEDSTFDYFPWYHQFPGESPALLIAIRPVSNKKEDGR
FTIFFNKREKKFSLHIADSQPGDSATYFCAASDNRIFFGDGTQLVVKPNIQNPEPAVYQL
KDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKTVLDMKAMDSKSNGAIAWSNQTSFT
CQDIF

Sequence of entity 2 (B, F), FASTA

>3C6L_2 TCR 2W20 beta chain (chains B, F)
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQENFSLILELATPSQTSVYFCASGDAWGYEQYFGPGTRLTVLEDLRDVTPPK
VSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSY
CLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQDISAEAWGRAD

Sequence of entity 3 (C, G), FASTA

>3C6L_3 H-2 class II histocompatibility antigen, A-B alpha chain (chains C, G)
IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG
LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE
PE

Sequence of entity 4 (D, H), FASTA

>3C6L_4 3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain) (chains D, H)
FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWKA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Primary citation

Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules. Dai, S., Huseby, E.S., Rubtsova, K. et al. Immunity (2008) 28:324-334. DOI 10.1016/j.immuni.2008.01.008 · PubMed

Other PDB entries of the same protein (UniProt P01849 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
2Q86 1.85 Å, Structure of the mouse invariant NKT cell receptor Valpha14
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
5M01 1.95 Å, Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from…
1LP9 2.0 Å, Xenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1
8WTE 2.17 Å, Crystal structure of TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide…
8WUL 2.36 Å, Crystal structure of affinity enhanced TCR in complex with HLA-A*11:01 bound to…
2JCC 2.5 Å, AH3 recognition of mutant HLA-A2 W167A
1NFD 2.8 Å, An alpha-beta T cell receptor (TCR) heterodimer in complex with an anti-TCR FAB fragment…
2J8U 2.88 Å, Large CDR3a loop alteration as a function of MHC mutation.
3MBE 2.89 Å, TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
6MF8 TCR alpha transmembrane domain

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