3C60: Mouse MHC class II I-Ab/3K peptide

Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR YAe62. Determined by X-ray diffraction at 3.05 Å resolution. Released 29 Apr 2008.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Mus musculus
Chains: 8
Atoms: 13,102
Mol. weight: 188.23 kDa
Released: 29 Apr 2008

Explore 3C60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C60 contains 40 α-helices and 164 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: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	9-13	5	2
β-strand	16-20	5	3
β-strand	23	1	4
β-strand	25	1	1
β-strand	31-37	7	2
β-strand	44-49	6	2
β-strand	55-58	4	3
β-strand	61-64	4	3
β-strand	66	1	4
β-strand	71	1	4
β-strand	74-79	6	3
α-helix	81-83	3
β-strand	85-92	8	2
β-strand	100-101	2	2
β-strand	105-110	6	2
β-strand	119-125	7	5
β-strand	132-137	6	5
β-strand	153-155	3	5
β-strand	161-163	3	6
α-helix	164-166	3
β-strand	168-170	3	6
β-strand	174-177	4	5
β-strand	198	1	5

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	7
β-strand	8-12	5	8
β-strand	17-19	3	9
β-strand	20-23	4	7
β-strand	29-36	8	8
β-strand	40-47	8	8
β-strand	54-55	2	8
β-strand	63-65	3	9
β-strand	71	1	7
β-strand	73-76	4	9
α-helix	81-83	3
β-strand	85-92	8	8
α-helix	94-96	3
β-strand	99-101	3	8
β-strand	106-110	5	8
β-strand	117	1	10
β-strand	120-125	6	5
α-helix	126-127	2
α-helix	128-133	6
β-strand	136-138	3	11
β-strand	140-144	5	5
β-strand	147	1	10
β-strand	151-157	7	12
β-strand	160-161	2	12
β-strand	166-168	3	5
β-strand	173-174	2	5
β-strand	184-190	7	5
β-strand	191-193	3	11
α-helix	194-197	4
β-strand	204-210	7	12
β-strand	213	1	13
β-strand	227	1	13
β-strand	229-235	7	12

Chains C and G: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-16	12	14
β-strand	20-27	8	14
β-strand	30-36	7	14
β-strand	41-44	4	14
α-helix	49-52	4
β-strand	54	1	15
α-helix	58-77	20
α-helix	82-85	4
β-strand	89	1	16
β-strand	92-94	3	17
β-strand	104-113	10	17
β-strand	119-124	6	18
β-strand	127-129	3	18
β-strand	133-135	3	17
α-helix	138	1
β-strand	139-140	2	17
β-strand	146-154	9	17
β-strand	162-167	6	18
β-strand	175-179	5	18

Chain D: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	15
α-helix	3-4	2
α-helix	8-12	5
β-strand	33-44	12	14
α-helix	46-48	3
β-strand	49-58	10	14
β-strand	62-67	6	14
β-strand	73-75	3	14
α-helix	78-80	3
α-helix	81-89	9
α-helix	91-100	10
α-helix	101-106	6
α-helix	107-108	2
α-helix	109-113	5
β-strand	122	1	19
β-strand	125	1	20
β-strand	128-130	3	20
β-strand	140-147	8	20
β-strand	150	1	19
β-strand	155-159	5	21
β-strand	164-165	2	21
β-strand	169-171	3	20
β-strand	183-190	8	20
β-strand	197-203	7	21
β-strand	211-216	6	21

Chain E: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	22
β-strand	9-13	5	23
β-strand	16-20	5	24
β-strand	23	1	25
β-strand	25	1	22
β-strand	31-37	7	23
β-strand	44-49	6	23
β-strand	55-58	4	24
β-strand	61-64	4	24
β-strand	66	1	25
β-strand	71	1	25
β-strand	74-79	6	24
α-helix	81-83	3
β-strand	85-92	8	23
β-strand	100-101	2	23
β-strand	105-110	6	23
α-helix	111-112	2
β-strand	119-125	7	26
β-strand	132-137	6	26
β-strand	153-155	3	26
β-strand	161-163	3	27
α-helix	164-166	3
β-strand	168-170	3	27
β-strand	174-177	4	26
β-strand	198	1	26

Chain F: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	28
β-strand	8-12	5	29
β-strand	17-19	3	30
β-strand	20-23	4	28
β-strand	29-35	7	29
β-strand	41-47	7	29
β-strand	54-55	2	29
β-strand	63-65	3	30
β-strand	71	1	28
β-strand	73-76	4	30
α-helix	81-83	3
β-strand	85-92	8	29
α-helix	94-96	3
β-strand	99-101	3	29
β-strand	106-110	5	29
β-strand	117	1	31
β-strand	120-121	2	32
β-strand	124-125	2	26
α-helix	126-127	2
α-helix	128-133	6
β-strand	136-138	3	33
β-strand	140	1	26
β-strand	141-144	4	32
β-strand	147	1	31
β-strand	151-157	7	34
β-strand	160-161	2	34
β-strand	166-168	3	32
β-strand	173-174	2	32
β-strand	184-190	7	32
β-strand	191-193	3	33
α-helix	194-197	4
β-strand	204-210	7	34
β-strand	213	1	35
β-strand	227	1	35
β-strand	229-235	7	34

Chain H: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	37
α-helix	8-12	5
β-strand	33-44	12	36
α-helix	46-48	3
β-strand	49-58	10	36
β-strand	61-67	7	36
β-strand	73-75	3	36
α-helix	78-80	3
α-helix	81-89	9
α-helix	91-100	10
α-helix	101-106	6
α-helix	107-108	2
α-helix	109-113	5
β-strand	122	1	41
β-strand	125	1	20
β-strand	128-130	3	20
β-strand	140-147	8	20
β-strand	150	1	41
β-strand	155-159	5	42
β-strand	164-165	2	42
β-strand	169-171	3	20
β-strand	183-190	8	20
β-strand	197-203	7	42
β-strand	211-216	6	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR YAe62 alpha chain	A, E	protein	199	Mus musculus
TCR YAe62 beta chain	B, F	protein	236	Mus musculus
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

>3C60_1 TCR YAe62 alpha chain (chains A, E)
DSVTQMQGQVTLSENDFLFINCTYSTTGYPTLFWYVQYSGEGPQLLLQVTTANNKGSSRG
FEATYDKGTTSFHLQKTSVQEIDSAVYYCAANSGTYQRFGTGTKLQVVPNIQNPDPAVYQ
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPS

Sequence of entity 2 (B, F), FASTA

>3C60_2 TCR YAe62 beta chain (chains B, F)
AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPD
GYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW

Sequence of entity 3 (C, G), FASTA

>3C60_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

>3C60_4 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain) (chains D, H)
FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWKA

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 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

Browse structure collections

About this viewer

MolViewer shows 3C60 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.