4AEN: PDB entry 4AEN

HLA-DR1 with covalently linked CLIP106-120 in reversed orientation. Determined by X-ray diffraction at 2.2 Å resolution. Released 1 Aug 2012.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 3,309
Mol. weight: 48.31 kDa
Released: 1 Aug 2012

Explore 4AEN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4AEN contains 13 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: 5 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	46-50	5
β-strand	52-53	2	2
α-helix	56-76	21
α-helix	80-84	5
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	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	161-166	6	5
β-strand	174-178	5	5

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	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	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-103	6	7
β-strand	114-122	9	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-138	3	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-162	8	7
β-strand	171-176	6	8
β-strand	184-188	5	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	107-113	7
β-strand	116-117	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, dr alpha chain	A	protein	207	HOMO SAPIENS	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-1 beta chain	B	protein	199	HOMO SAPIENS	P01911 (AlphaFold model)
HLA class II histocompatibility antigen gamma chain	C	protein	16	HOMO SAPIENS	P04233 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4AEN_1 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN (chains A)
GGGGSGGGGSGGGGSIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRL
EEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVL
ICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRV
EHWGLDEPLLKHWEFDAPSPLPETTEN

Sequence of entity 2 (B), FASTA

>4AEN_2 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN (chains B)
MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAE
YWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSV
SGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPS
VTSPLTVEWRARSESAQSK

Sequence of entity 3 (C), FASTA

>4AEN_3 HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN (chains C)
MKMRMATPLLMQALPM

Primary citation

Peptide Linkage to the Alpha-Subunit of Mhcii Creates a Stably Inverted Antigen Presentation Complex. Schlundt, A., Gunther, S., Sticht, J. et al. J Mol Biol (2012) 423:294. DOI 10.1016/J.JMB.2012.07.008 · 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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