1K2D: Autoimmune MHC class II I-Au

Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A. Determined by X-ray diffraction at 2.2 Å resolution. Released 4 Mar 2003.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,597
Mol. weight: 46.95 kDa
Ligands: NAG
Released: 4 Mar 2003

Explore 1K2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K2D contains 11 α-helices and 32 β-strands across 3 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, 14 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	46-50	5
β-strand	53	1	2
α-helix	56-76	21
α-helix	80-84	5
β-strand	88-93	6	3
β-strand	103-112	10	3
β-strand	118-123	6	4
β-strand	126-128	3	4
β-strand	132-134	3	3
α-helix	137	1
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: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	1
β-strand	18	1	5
β-strand	21	1	5
β-strand	25-32	8	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	52-57	6
α-helix	58-74	15
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-86	5
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-103	6	7
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	2	8
β-strand	142-144	3	7
α-helix	145-147	3
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	-2	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-U alpha chain	A	protein	189	Mus musculus	P14438 (AlphaFold model)
H-2 class II histocompatibility antigen, A-U beta chain	B	protein	189	Mus musculus	P06344 (AlphaFold model)
Myelin Basic Protein peptide with 8 residue linker peptide	P	protein	23		P02686 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1K2D_1 H-2 class II histocompatibility antigen, A-U alpha chain (chains A)
HSRGEDDIEADHVGSYGIVVYQSPGDIGQYTFEFDGDELFYVDLDKKETIWMLPEFAQLR
SFDPQGGLQNIATGKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNI
FPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEE
PVLKHWEPE

Sequence of entity 2 (B), FASTA

>1K2D_2 H-2 class II histocompatibility antigen, A-U beta chain (chains B)
GDSERHFVVQFQPFCYFTNGTQRIRYVTRYIYNREEYLRFDSDVGEYRAVTELGRPDAEY
YNKQYLERTRAELDTVCRYNYEETEVPTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTD
FYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLK
SPITVEWRA

Sequence of entity 3 (P), FASTA

>1K2D_3 Myelin Basic Protein peptide with 8 residue linker peptide (chains P)
HSRGGASQYRPSQRHGTGSGSGS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au. He, X.L., Radu, C., Sidney, J. et al. Immunity (2002) 17:83-94. DOI 10.1016/S1074-7613(02)00340-0 · PubMed

Other PDB entries of the same protein (UniProt P14438 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2P24 2.15 Å, I-Au/MBP125-135
2PXY 2.23 Å, Crystal structures of immune receptor complexes
1U3H 2.42 Å, Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A
2Z31 2.7 Å, Crystal structure of immune receptor complex

Browse structure collections

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