3CUP: MHC class II molecule I-Ag7

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235. Determined by X-ray diffraction at 3.09 Å resolution. Released 21 Apr 2009.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Mus musculus
Chains: 2
Atoms: 2,953
Mol. weight: 47.62 kDa
Ligands: NAG
Released: 21 Apr 2009

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

Secondary structure: helices and β-sheets

3CUP contains 12 α-helices and 31 β-strands across 2 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
β-strand	53	1	2
α-helix	57-76	20
α-helix	81-83	3
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	127-128	2	5
β-strand	132-134	3	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	223	1	2
β-strand	248-259	12	1
β-strand	264-273	10	1
β-strand	276-282	7	1
β-strand	289-290	2	1
α-helix	293-295	3
α-helix	296-311	16
α-helix	313	1
α-helix	314-318	5
α-helix	319-321	3
α-helix	322-326	5
α-helix	330-332	3
β-strand	335	1	6
β-strand	338-343	6	7
β-strand	355-362	8	7
β-strand	363	1	6
β-strand	368-371	4	8
β-strand	383-384	2	7
α-helix	385-387	3
β-strand	388-389	2	7
β-strand	395-400	6	7
β-strand	412-416	5	8
β-strand	424-427	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-D alpha chain	A	protein	190	Mus musculus	P04228 (AlphaFold model)
MHC class II H2-IA-beta chain linked to GAD221-235 peptide	B	protein	222	Mus musculus	Q05683 (AlphaFold model), Q31135 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3CUP_1 H-2 class II histocompatibility antigen, A-D alpha chain (chains A)
EDDIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEP
QGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPV
INITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLK
HWSSADLVPR

Sequence of entity 2 (B), FASTA

>3CUP_2 MHC class II H2-IA-beta chain linked to GAD221-235 peptide (chains B)
GSHSRGLKKMREIIGWPGGSGGSGSGSGDSERHFVHQFKGECYFTNGTQRIRLVTRYIYN
REEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRL
EQPNVAISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWT
FQVLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWSSADLVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (EPE) are not listed.

Primary citation

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235. Yoshida, K., Corper, A.L., Puckett, C. et al. To be published.

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…
3MBE 2.89 Å, TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
7RDV 2.9 Å, TFH TCR bound to MHC Class II IAd presenting aggrecan epitope
1F3J 3.1 Å, Histocompatibility antigen I-AG7

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