3C5Z: Mouse MHC class II I-Ab/3K peptide

Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506. Determined by X-ray diffraction at 2.55 Å resolution. Released 29 Apr 2008.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Mus musculus
Chains: 8
Atoms: 13,288
Mol. weight: 189.92 kDa
Released: 29 Apr 2008

Explore 3C5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C5Z contains 52 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: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	9-13	5	2
β-strand	18-20	3	3
β-strand	22-24	3	1
α-helix	30	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	1
β-strand	71	1	1
β-strand	74-76	3	3
α-helix	81-83	3
β-strand	85-93	9	2
β-strand	98-101	4	2
β-strand	105-110	6	2
β-strand	119-123	5	4
β-strand	124-125	2	5
β-strand	132-137	6	4
α-helix	146-148	3
β-strand	153-155	3	4
α-helix	156-158	3
β-strand	161-163	3	6
β-strand	168-170	3	6
β-strand	172-177	6	4
α-helix	184-187	4
β-strand	198	1	4

Chain B: 6 helices, 26 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
β-strand	100-101	2	8
β-strand	105-110	6	8
α-helix	113-115	3
β-strand	117	1	10
β-strand	120-125	6	5
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	5
β-strand	147	1	10
β-strand	151-157	7	11
β-strand	160-162	3	11
β-strand	166-168	3	5
β-strand	173-174	2	5
β-strand	184-193	10	5
α-helix	194-197	4
β-strand	203-210	8	11
β-strand	213	1	12
β-strand	227	1	12
β-strand	229-236	8	11
α-helix	237-238	2

Chains C and G: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-16	12	13
β-strand	20-27	8	13
β-strand	30-36	7	13
β-strand	41-44	4	13
α-helix	47-52	6
β-strand	54	1	14
α-helix	58-76	19
α-helix	81-83	3
β-strand	89-94	6	15
β-strand	104-113	10	15
β-strand	119-124	6	16
β-strand	129	1	16
β-strand	133-135	3	15
α-helix	138	1
β-strand	139-140	2	15
β-strand	146-154	9	15
β-strand	162-167	6	16
β-strand	175-179	5	16

Chain D: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	14
α-helix	3-4	2
α-helix	6-13	8
β-strand	33-44	12	13
β-strand	49-58	10	13
β-strand	61-67	7	13
β-strand	72-75	4	13
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
α-helix	114-115	2
α-helix	117-119	3
β-strand	122	1	17
β-strand	125-130	6	18
α-helix	133-134	2
β-strand	140-149	10	18
β-strand	150	1	17
β-strand	155-160	6	19
β-strand	163-165	3	19
β-strand	169-171	3	18
β-strand	175-176	2	18
β-strand	182-190	9	18
β-strand	197-203	7	19
β-strand	211-216	6	19

Chain E: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	20
β-strand	9-13	5	21
β-strand	18-20	3	22
β-strand	22-24	3	20
α-helix	30	1
β-strand	31-37	7	21
β-strand	44-49	6	21
β-strand	55-58	4	22
β-strand	61-64	4	22
β-strand	66	1	20
β-strand	71	1	20
β-strand	74-76	3	22
α-helix	81-83	3
β-strand	85-93	9	21
β-strand	98-101	4	21
β-strand	105-110	6	21
β-strand	119-123	5	23
β-strand	124-125	2	24
β-strand	132-137	6	23
α-helix	146-148	3
β-strand	153-155	3	23
α-helix	156-158	3
β-strand	159-163	5	23
β-strand	168-177	10	23
α-helix	184-187	4
β-strand	198	1	23

Chain F: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	25
β-strand	8-12	5	26
β-strand	17-19	3	27
β-strand	20-23	4	25
β-strand	29-36	8	26
β-strand	40-47	8	26
β-strand	54-55	2	26
β-strand	63-65	3	27
β-strand	71	1	25
β-strand	73-76	4	27
α-helix	81-83	3
β-strand	85-92	8	26
β-strand	100-101	2	26
β-strand	105-110	6	26
β-strand	117	1	28
β-strand	120-125	6	24
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	24
β-strand	147	1	28
β-strand	151-157	7	29
β-strand	160-162	3	29
β-strand	166-168	3	24
β-strand	173-174	2	24
β-strand	184-193	10	24
α-helix	194-197	4
β-strand	203-210	8	29
β-strand	213	1	30
α-helix	224-225	2
β-strand	227	1	30
β-strand	229-236	8	29

Chain H: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	32
α-helix	3-4	2
α-helix	6-13	8
β-strand	33-44	12	31
β-strand	49-58	10	31
β-strand	61-67	7	31
β-strand	72-73	2	31
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
α-helix	114-115	2
α-helix	117-119	3
β-strand	122	1	35
β-strand	125-130	6	18
α-helix	133-134	2
β-strand	140-149	10	18
β-strand	150	1	35
β-strand	155-160	6	36
β-strand	163-165	3	36
β-strand	169-171	3	18
α-helix	173-174	2
β-strand	175-176	2	18
β-strand	182-190	9	18
β-strand	197-203	7	36
β-strand	211-216	6	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR B3K506 Alpha Chain	A, E	protein	202	Mus musculus
TCR B3K506 Beta Chain	B, F	protein	240	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

>3C5Z_1 TCR B3K506 Alpha Chain (chains A, E)
DSVTQTEGNVALSEEDFLTIHCNYSASGYPALFWYVQYPGEGPQFLFRASRDKEKGSSRG
FEATYDKGTTSFHLRKASVQESDSAVYYCALVISNTNKVVFGTGTRLQVLPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSP

Sequence of entity 2 (B, F), FASTA

>3C5Z_2 TCR B3K506 Beta Chain (chains B, F)
AVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPD
GYKASRPSQENFSLILELASLSQTAVYFCASIDSSGNTLYFGEGSRLIVVEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Sequence of entity 3 (C, G), FASTA

>3C5Z_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

>3C5Z_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
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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