3MBE: TCR 21.30

TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27). Determined by X-ray diffraction at 2.89 Å resolution. Released 12 May 2010.

Method: X-ray diffraction
Resolution: 2.89 Å
Organisms: Mus musculus, Gallus gallus
Chains: 10
Atoms: 13,028
Mol. weight: 203.93 kDa
Ligands: NAG
Released: 12 May 2010

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

Secondary structure: helices and β-sheets

3MBE contains 28 α-helices and 162 β-strands across 10 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, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	11-15	5	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	48-51	4
β-strand	53-54	2	2
α-helix	57-76	20
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-127	2	4
β-strand	132-134	3	3
β-strand	138-139	2	3
β-strand	145-153	9	3
β-strand	161-166	6	4
β-strand	174-178	5	4

Chain B: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-47	2	1
α-helix	52-54	3
α-helix	57-74	16
α-helix	75-79	5
α-helix	80-81	2
α-helix	82-87	6
β-strand	95	1	5
β-strand	98-101	4	6
β-strand	113-114	2	7
β-strand	117-120	4	6
β-strand	123	1	5
β-strand	128-133	6	8
β-strand	136-138	3	8
β-strand	148-149	2	6
β-strand	155-159	5	6
β-strand	162-163	2	7
β-strand	171-176	6	8
β-strand	184-188	5	8

Chains C and G: 1 helix, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-14	5	10
β-strand	19-25	7	9
β-strand	39-44	6	11
β-strand	50	1	11
β-strand	54-56	3	11
β-strand	65-69	5	9
β-strand	79-84	6	9
β-strand	86-91	6	9
β-strand	100	1	10
β-strand	101-107	7	11
β-strand	116-118	3	11
β-strand	123-127	5	10
β-strand	136-141	6	12
β-strand	149-154	6	12
α-helix	161-162	2
β-strand	170-172	3	12
β-strand	178	1	13
β-strand	187	1	13
β-strand	189-194	6	12

Chain D: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	14
β-strand	10-14	5	15
β-strand	19-21	3	16
β-strand	22-24	3	14
β-strand	38-44	7	15
β-strand	50-58	9	15
β-strand	65-68	4	15
β-strand	77-79	3	16
β-strand	86	1	14
β-strand	88-91	4	16
β-strand	101	1	15
β-strand	104-107	4	15
β-strand	117-118	2	15
β-strand	123-127	5	15
α-helix	130-132	3
β-strand	134	1	17
β-strand	137-141	5	18
β-strand	142	1	12
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	18
β-strand	164	1	17
β-strand	168-174	7	19
β-strand	177-179	3	19
β-strand	183-185	3	18
β-strand	193	1	20
β-strand	196	1	20
β-strand	197-206	10	18
α-helix	207-211	5
β-strand	216-223	8	19
β-strand	226	1	21
α-helix	237-238	2
β-strand	240	1	21
β-strand	242-249	8	19

Chain E: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	22
β-strand	11-15	5	22
β-strand	19-26	8	22
β-strand	29-35	7	22
β-strand	40-43	4	22
α-helix	48-51	4
β-strand	53-54	2	23
α-helix	57-76	20
β-strand	85	1	24
β-strand	88-93	6	25
β-strand	103-112	10	25
β-strand	113	1	24
β-strand	118-123	6	26
β-strand	126-127	2	26
β-strand	132-134	3	25
β-strand	138-139	2	25
β-strand	145-153	9	25
β-strand	161-166	6	26
β-strand	174-178	5	26

Chain F: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	22
β-strand	24-32	9	22
β-strand	35-41	7	22
β-strand	46-47	2	22
α-helix	52-54	3
α-helix	57-74	16
α-helix	75-79	5
α-helix	80-81	2
α-helix	82-87	6
β-strand	95	1	27
β-strand	98-101	4	28
β-strand	113-114	2	29
β-strand	117-120	4	28
β-strand	123	1	27
β-strand	128-133	6	30
β-strand	136-138	3	30
β-strand	148-149	2	28
β-strand	155-159	5	28
β-strand	162-163	2	29
β-strand	171-176	6	30
β-strand	184-188	5	30

Chain H: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	36
β-strand	10-14	5	37
β-strand	19-21	3	38
β-strand	22-24	3	36
β-strand	38-44	7	37
β-strand	50-58	9	37
β-strand	65-68	4	37
β-strand	77-79	3	38
β-strand	86	1	36
β-strand	88-91	4	38
β-strand	100-101	2	37
β-strand	104-107	4	37
β-strand	117-118	2	37
β-strand	123-127	5	37
α-helix	130-132	3
β-strand	134	1	39
β-strand	137-141	5	40
β-strand	142	1	34
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	40
β-strand	164	1	39
β-strand	168-174	7	41
β-strand	177-179	3	41
β-strand	183-185	3	40
β-strand	193	1	42
β-strand	196	1	42
β-strand	197-206	10	40
α-helix	207-211	5
β-strand	216-223	8	41
β-strand	226	1	43
α-helix	237-238	2
β-strand	240	1	43
β-strand	242-249	8	41

Chains P and Q: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	13-14	2	2
α-helix	20-23	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II H2-IAg7 alpha chain	A, E	protein	190	Mus musculus	P04228 (AlphaFold model)
MHC class II H2-IAg7 beta chain	B, F	protein	201	Mus musculus	Q31135 (AlphaFold model)
Peptide hel 11-27	P, Q	protein	18	Gallus gallus	P00698 (AlphaFold model)
TCR 21.3 alpha chain	C, G	protein	229	Mus musculus	P01849 (AlphaFold model)
TCR 21.3 beta chain	D, H	protein	259	Mus musculus	P01852

Sequence of entity 1 (A, E), FASTA

>3MBE_1 MHC CLASS II H2-IAg7 ALPHA CHAIN (chains A, E)
EDDIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEP
QGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPV
INITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLK
HWSSADLVPR

Sequence of entity 2 (B, F), FASTA

>3MBE_2 MHC CLASS II H2-IAg7 BETA CHAIN (chains B, F)
GSGSGSGDSERHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELG
RHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSRTEALNHHNTL
VCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHV
EHPSLKSPITVEWSSADLVPR

Sequence of entity 3 (P, Q), FASTA

>3MBE_3 PEPTIDE HEL 11-27 (chains P, Q)
GAMKRHGLDNYRGYSLGN

Sequence of entity 4 (C, G), FASTA

>3MBE_4 TCR 21.3 alpha chain (chains C, G)
GMPVEQNPPALSLYEGADSGLRCNFSTTMKSVQWFQQNHRGRLITLFYLAQGTKENGRLK
STFNSKERYSTLHIKDAQLEDSGTYFCAAEDGGSGNKLIFGTGTLLSVKPNIQNPEPAVY
QLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGAIAWSNQTS
FTCQDIFKETNATYPSSDVPCDATLTEKSFETDMNLNFQNLSSADLVPR

Sequence of entity 5 (D, H), FASTA

>3MBE_5 TCR 21.3 beta chain (chains D, H)
EAAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDI
PDGYKASRPSQENFSLILELASLSQTAVYFCASSWDRAGNTLYFGEGSRLIVVEDLRNVT
PPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESN
YSYSLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADC
GITSASYHQSSADLVPRGS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

The diabetogenic mouse MHC class II molecule I-Ag7 is endowed with a switch that modulates TCR affinity. Yoshida, K., Corper, A.L., Herro, R. et al. J Clin Invest (2010) 120:1578-1590. DOI 10.1172/JCI41502 · PubMed

Other PDB entries of the same protein (UniProt P04228 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BLQ 1.8 Å, Crystal Structure of IAg7 in complex with insulin mimotope p8E9E
7QHP 1.82 Å, Structure of I-Ag7 with a bound hybrid insulin peptide
6BLR 1.96 Å, Crystal Structure of IAg7 in complex with insulin mimotope p8E9E6SS
6BLX 2.32 Å, Crystal structure of IAg7 in complex with insulin mimotope p8G9E
2IAD 2.4 Å, Class II MHC I-ad in complex with an influenza hemagglutinin peptide 126-138
5DMK 2.45 Å, Crystal Structure of IAg7 in complex with RLGL-WE14
1ES0 2.6 Å, Crystal structure of the murine class II allele I-A(G7) complexed with the glutamic acid…
1IAO 2.6 Å, Class II MHC I-ad in complex with ovalbumin peptide 323-339
7Z50 2.65 Å, Structure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin…
7RDV 2.9 Å, TFH TCR bound to MHC Class II IAd presenting aggrecan epitope
3CUP 3.09 Å, Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide…
1F3J 3.1 Å, Histocompatibility antigen I-AG7

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