2OJE: Mycoplasma arthritidis-derived mitogen

Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of EDTA. Determined by X-ray diffraction at 3.0 Å resolution. Released 23 Jan 2007.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Mycoplasma arthritidis
Chains: 8
Atoms: 10,010
Mol. weight: 140.62 kDa
Ligands: PO4
Released: 23 Jan 2007

Explore 2OJE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OJE contains 45 α-helices and 64 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.

Chain A: 3 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	46-49	4
β-strand	53	1	2
α-helix	56-76	21
α-helix	80-82	3
β-strand	85	1	3
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
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	161-166	6	5
β-strand	174-178	5	5

Chains B and F: 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	46-49	4	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
β-strand	98-104	7	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	170-176	7	8
α-helix	183	1
β-strand	184-189	6	8

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	2

Chain D: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	1-3	3
α-helix	24-25	2
α-helix	26-33	8
α-helix	44-66	23
α-helix	72-92	21
α-helix	97-123	27
α-helix	126-145	20
α-helix	158-167	10
α-helix	171-175	5
α-helix	177-194	18
α-helix	200-203	4
α-helix	205-210	6

Chain E: 3 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	46-49	4
β-strand	53	1	10
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	11
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	161-166	6	13
β-strand	174-178	5	13

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	10
α-helix	308-310	3

Chain H: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	1-3	3
α-helix	24-25	2
α-helix	26-33	8
α-helix	44-66	23
α-helix	72-92	21
α-helix	97-123	27
α-helix	126-145	20
α-helix	158-167	10
α-helix	171-175	5
α-helix	177-194	18
α-helix	200-202	3
α-helix	205-210	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain precursor	A, E	protein	180	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-1 beta chain precursor	B, F	protein	190	Homo sapiens	P01911 (AlphaFold model)
haemagglutinin peptide 306-318	C, G	protein	13		Q91LS8
Superantigen	D, H	protein	214	Mycoplasma arthritidis	Q48898 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>2OJE_1 HLA class II histocompatibility antigen, DR alpha chain precursor (chains A, E)
KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALA
NIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTW
LRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD

Sequence of entity 2 (B, F), FASTA

>2OJE_2 HLA class II histocompatibility antigen, DRB1-1 beta chain precursor (chains B, F)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C, G), FASTA

>2OJE_3 haemagglutinin peptide 306-318 (chains C, G)
PKYVKQNTLKLAT

Sequence of entity 4 (D, H), FASTA

>2OJE_4 Superantigen (chains D, H)
SMKLRVENPKKAQKHFVQNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHA
FGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLS
YFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWF
RSLLVKGVYLIKRYYEGDIELKTTSDFAKAVFED

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4

Primary citation

Zinc induces dimerization of the class II major histocompatibility complex molecule that leads to cooperative binding to a superantigen. Li, H., Zhao, Y., Guo, Y. et al. J Biol Chem (2007) 282:5991-6000. DOI 10.1074/jbc.M608482200 · 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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