1LNU: Class II MHC molecule iab

Crystal structure of class II MHC molecule iab bound to EALPHA3K peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 14 Aug 2002.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Mus musculus
Chains: 8
Atoms: 13,265
Mol. weight: 184.8 kDa
Ligands: NAG
Released: 14 Aug 2002

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

Secondary structure: helices and β-sheets

1LNU contains 56 α-helices and 116 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.

Chains A, C and E: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-15	10	1
β-strand	20-27	8	1
β-strand	30-36	7	1
β-strand	41-44	4	1
α-helix	47-52	6
β-strand	54	1	2
α-helix	57-77	21
α-helix	81-85	5
β-strand	91-94	4	3
β-strand	104-113	10	3
β-strand	118-124	7	4
β-strand	133-135	3	3
α-helix	136-138	3
β-strand	139-140	2	3
β-strand	146-154	9	3
β-strand	162-168	7	4
β-strand	175-179	5	4

Chains B, F and H: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	2
α-helix	3-7	5
α-helix	9-12	4
β-strand	34-42	9	1
β-strand	51-58	8	1
β-strand	61-67	7	1
β-strand	72-75	4	1
α-helix	78-80	3
α-helix	81-89	9
α-helix	91-97	7
α-helix	100-103	4
α-helix	106-108	3
α-helix	109-113	5
α-helix	117-119	3
β-strand	122	1	5
α-helix	123-124	2
β-strand	125-131	7	6
β-strand	141-149	9	6
β-strand	150	1	5
β-strand	155-160	6	7
β-strand	163-165	3	7
β-strand	169-171	3	6
β-strand	176	1	6
β-strand	182-189	8	6
β-strand	198-203	6	7
β-strand	211-215	5	7

Chain D: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
α-helix	3-7	5
α-helix	9-12	4
β-strand	34-42	9	8
β-strand	51-58	8	8
β-strand	61-67	7	8
β-strand	72-75	4	8
α-helix	78-80	3
α-helix	81-89	9
α-helix	91-97	7
α-helix	100-103	4
α-helix	106-108	3
α-helix	109-113	5
α-helix	117-119	3
β-strand	122	1	12
α-helix	123-124	2
β-strand	125-131	7	13
β-strand	141-149	9	13
β-strand	150	1	12
β-strand	155-160	6	14
β-strand	163-164	2	14
β-strand	169-171	3	13
β-strand	176	1	13
β-strand	182-189	8	13
β-strand	198-203	6	14
β-strand	211-215	5	14

Chain G: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-15	10	21
β-strand	20-27	8	21
β-strand	30-36	7	21
β-strand	41-44	4	21
α-helix	47-50	4
β-strand	54	1	22
α-helix	57-77	21
α-helix	81-85	5
β-strand	91-94	4	23
β-strand	104-113	10	23
β-strand	118-124	7	24
β-strand	133-135	3	23
α-helix	136-138	3
β-strand	139-140	2	23
β-strand	146-154	9	23
β-strand	162-168	7	24
β-strand	175-179	5	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class II histocompatibility antigen, A-B alpha chain	A, C, E, G	protein	182	Mus musculus	P14434 (AlphaFold model)
H-2 class II histocompatibility antigen, A beta chain	B, D, F, H	protein	217	Mus musculus	P14483 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>1LNU_1 H-2 class II histocompatibility antigen, A-B alpha chain (chains A, C, E, G)
IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG
LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE
PE

Sequence of entity 2 (B, D, F, H), FASTA

>1LNU_2 H-2 class II histocompatibility antigen, A beta chain (chains B, D, F, H)
FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWKA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Alternate interactions define the binding of peptides to the MHC molecule IA(b). Liu, X., Dai, S., Crawford, F. et al. Proc Natl Acad Sci U S A (2002) 99:8820-8825. DOI 10.1073/pnas.132272099 · 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
3C5Z 2.55 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
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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