1A6A: Intermediate in class II MHC maturation: clip

The structure of an intermediate in class II MHC maturation: clip bound to HLA-DR3. Determined by X-ray diffraction at 2.75 Å resolution. Released 27 May 1998.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,158
Mol. weight: 44.52 kDa
Ligands: NAG
Released: 27 May 1998

Explore 1A6A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1A6A contains 11 α-helices and 33 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	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	52-53	2	2
α-helix	56-76	21
α-helix	80-82	3
β-strand	85	1	3
β-strand	90-93	4	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-127	2	5
β-strand	133-134	2	4
α-helix	137	1
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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	6
β-strand	98-103	6	7
β-strand	114-120	7	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136	1	8
β-strand	142-143	2	7
β-strand	148-149	2	7
β-strand	155-158	4	7
β-strand	160-162	3	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	89-90	2	2
α-helix	96-100	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	176	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DR-1 beta chain	B	protein	187	Homo sapiens	P01911 (AlphaFold model)
HLA class II histocompatibility antigen, gamma chain	C	protein	15	Homo sapiens	P04233 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1A6A_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIA
VDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRN
GKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF

Sequence of entity 2 (B), FASTA

>1A6A_2 HLA class II histocompatibility antigen, DR-1 beta chain (chains B)
PRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPDAEYWNSQ
KDLLEQKRGRVDNYCRHNYGVVESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCSVSGFYP
GSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPL
TVEWRAR

Sequence of entity 3 (C), FASTA

>1A6A_3 HLA class II histocompatibility antigen, gamma chain (chains C)
PVSKMRMATPLLMQA

Ligands and cofactors

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

Primary citation

The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. Ghosh, P., Amaya, M., Mellins, E. et al. Nature (1995) 378:457-462. DOI 10.1038/378457a0 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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