1F3J: Histocompatibility antigen I-AG7

Histocompatibility antigen I-AG7. Determined by X-ray diffraction at 3.1 Å resolution. Released 20 Sept 2000.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Mus musculus, Gallus gallus
Chains: 6
Atoms: 6,464
Mol. weight: 90.62 kDa
Ligands: NAG
Released: 20 Sept 2000

Explore 1F3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1F3J contains 18 α-helices and 58 β-strands across 5 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	12	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	57-76	20
α-helix	80-84	5
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-127	2	3
β-strand	132-134	3	2
α-helix	135-137	3
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-166	6	3
β-strand	174-178	5	3

Chain B: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	1
β-strand	24-32	9	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	55-64	10
α-helix	68-74	7
α-helix	75-80	6
α-helix	81	1
α-helix	82-86	6
β-strand	95	1	4
β-strand	98	1	5
β-strand	101-103	3	5
β-strand	113-122	10	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-137	2	6
β-strand	142-145	4	5
β-strand	148-149	2	5
β-strand	155-163	9	5
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain D: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	12	7
β-strand	19-26	8	7
β-strand	29-35	7	7
β-strand	40-43	4	7
α-helix	57-76	20
α-helix	80-84	5
β-strand	88-93	6	8
β-strand	103-112	10	8
β-strand	118-123	6	9
β-strand	126-128	3	9
β-strand	132-134	3	8
α-helix	135-137	3
β-strand	138-139	2	8
β-strand	145-153	9	8
β-strand	161-166	6	9
β-strand	174-178	5	9

Chain E: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	7
β-strand	24-32	9	7
β-strand	35-41	7	7
β-strand	47-49	3	7
α-helix	55-64	10
α-helix	68-74	7
α-helix	75-80	6
α-helix	81	1
α-helix	82-86	6
α-helix	90-92	3
β-strand	95	1	10
β-strand	98-103	6	5
β-strand	113-122	10	5
β-strand	123	1	10
β-strand	128-133	6	11
β-strand	136-137	2	11
β-strand	142-145	4	5
β-strand	148-149	2	5
β-strand	155-163	9	5
β-strand	170-176	7	11
β-strand	184	1	11
β-strand	187-189	3	11

Chain Q: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	20-23	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen	A, D	protein	182	Mus musculus	P04228 (AlphaFold model)
MHC class II nod	B, E	protein	187	Mus musculus	Q31135 (AlphaFold model)
Lysozyme C	P, Q	protein	14	Gallus gallus	P00698 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1F3J_1 H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN (chains A, D)
IEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGG
LQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE
PE

Sequence of entity 2 (B, E), FASTA

>1F3J_2 MHC CLASS II NOD (chains B, E)
ERHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELGRHSAEYYNK
QYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSRTEALNHHNTLVCSVTDFYP
AKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHVEHPSLKSPI
TVEWRAQ

Sequence of entity 3 (P, Q), FASTA

>1F3J_3 LYSOZYME C (chains P, Q)
AMKRHGLDNYRGYS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice. Latek, R.R., Suri, A., Petzold, S.J. et al. Immunity (2000) 12:699-710. DOI 10.1016/S1074-7613(00)80220-4 · 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…
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
3CUP 3.09 Å, Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide…

Browse structure collections

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