7NZE: HLA-DR4

Crystal structure of HLA-DR4 in complex with a human collagen type II peptide. Determined by X-ray diffraction at 2.05 Å resolution. Released 8 Jun 2022.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,782
Mol. weight: 91.16 kDa
Ligands: NAG
Released: 8 Jun 2022

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

Secondary structure: helices and β-sheets

7NZE contains 30 α-helices and 62 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 AAA: 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	48-51	4
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 BBB: 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	65-74	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	113-122	10	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	155-163	9	7
α-helix	165-166	2
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain CCC: 6 helices, 15 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
α-helix	57-76	20
α-helix	81-84	4
β-strand	85	1	10
α-helix	86-87	2
β-strand	88-93	6	11
β-strand	103-112	10	11
β-strand	113	1	10
β-strand	118-123	6	12
β-strand	126-128	3	12
β-strand	133-134	2	11
α-helix	137	1
β-strand	138-139	2	11
β-strand	145-153	9	11
β-strand	160-166	7	12
α-helix	173	1
β-strand	174-179	6	12

Chain DDD: 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	46-49	4	9
α-helix	52-54	3
α-helix	55-61	7
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	13
α-helix	96-97	2
β-strand	98-103	6	14
β-strand	113-122	10	14
β-strand	123	1	13
β-strand	128-133	6	15
β-strand	136-138	3	15
β-strand	142-144	3	14
β-strand	148-149	2	14
β-strand	155-163	9	14
β-strand	170-176	7	15
β-strand	184-189	6	15

Chain EEE: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11-13	3

Chain FFF: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	2
α-helix	5-9	5
α-helix	11-13	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	AAA, CCC	protein	182	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen DR beta chain	BBB, DDD	protein	191	Homo sapiens	A2BFX2 (AlphaFold model)
Collagen alpha-1(II) chain	EEE, FFF	protein	15	Homo sapiens	P02458 (AlphaFold model)

Sequence of entity 1 (AAA, CCC), FASTA

>7NZE_1 HLA class II histocompatibility antigen, DR alpha chain (chains AAA, CCC)
KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLREFGRFASFEAQGALA
NIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTW
LRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD
AS

Sequence of entity 2 (BBB, DDD), FASTA

>7NZE_2 HLA class II histocompatibility antigen DR beta chain (chains BBB, DDD)
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVN
GFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSL
TSPLTVEWRAR

Sequence of entity 3 (EEE, FFF), FASTA

>7NZE_3 Collagen alpha-1(II) chain (chains EEE, FFF)
GIAGFKGEQGPKGEP

Ligands and cofactors

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

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

Primary citation

Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor. Ge, C., Weisse, S., Xu, B. et al. Ann Rheum Dis (2022) 81:480-489. DOI 10.1136/annrheumdis-2021-220500 · 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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