7YXB: PDB entry 7YXB

MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange. Determined by X-ray diffraction at 2.1 Å resolution. Released 22 Feb 2023.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,130
Mol. weight: 96.45 kDa
Ligands: FLC
Released: 22 Feb 2023

Explore 7YXB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YXB contains 27 α-helices and 64 β-strands across 6 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	5-15	11	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	81-84	4
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	126-128	3	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: 8 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	65-72	8
α-helix	74	1
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	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
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 C: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	9
β-strand	19-26	8	9
β-strand	29-35	7	9
β-strand	40-43	4	9
α-helix	48-51	4
β-strand	53	1	10
α-helix	56-76	21
α-helix	81-84	4
β-strand	85	1	11
α-helix	86-87	2
β-strand	88-93	6	12
β-strand	103-112	10	12
β-strand	113	1	11
β-strand	118-123	6	13
β-strand	126-128	3	13
β-strand	133-134	2	12
β-strand	138-139	2	12
β-strand	145-153	9	12
β-strand	160-166	7	13
β-strand	174-179	6	13

Chain D: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	9
β-strand	23-32	10	9
β-strand	35-41	7	9
β-strand	47-49	3	9
α-helix	52-54	3
α-helix	55-61	7
α-helix	65-71	7
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	14
β-strand	98-103	6	15
β-strand	113-122	10	15
β-strand	123	1	14
β-strand	128-133	6	16
β-strand	136-138	3	16
β-strand	142-144	3	15
β-strand	148-149	2	15
β-strand	155-163	9	15
β-strand	170-176	7	16
β-strand	184-189	6	16

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-7	2	2
α-helix	13-17	5

Chain H: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	10
α-helix	8-9	2
α-helix	13-15	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, C	protein	192	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen DR beta chain	B, D	protein	198	Homo sapiens	A0A1V1IGJ9 (AlphaFold model)
CLIP peptide	G, H	protein	20	Homo sapiens	P04233 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7YXB_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, C)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DAPSPLPETTEV

Sequence of entity 2 (B, D), FASTA

>7YXB_2 HLA class II histocompatibility antigen DR beta chain (chains B, D)
DTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEYW
NSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVNG
FYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSLT
SPLTVEWRARSESAQSKV

Sequence of entity 3 (G, H), FASTA

>7YXB_3 CLIP peptide (chains G, H)
AFAPVSKMRMATPLLMQAGN

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange. Abualrous, E.T., Stolzenberg, S., Sticht, J. et al. Nat Chem Biol (2023) 19:1196-1204. DOI 10.1038/s41589-023-01316-3 · 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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