1R5I: MAM-MHC complex

Crystal structure of the MAM-MHC complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 16 Mar 2004.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Mycoplasma arthritidis
Chains: 8
Atoms: 10,014
Mol. weight: 141.19 kDa
Ligands: PO4
Released: 16 Mar 2004

Explore 1R5I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1R5I contains 44 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.

Chains A and E: 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	80-84	5
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

Chain B: 6 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
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
β-strand	184-189	6	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	2
α-helix	315-317	3

Chains D and H: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	24-25	2
α-helix	26-33	8
α-helix	39-41	3
α-helix	42-66	25
α-helix	72-92	21
α-helix	97-123	27
α-helix	126-145	20
α-helix	158-166	9
α-helix	171-175	5
α-helix	177-194	18
α-helix	200-202	3
α-helix	205-210	6

Chain F: 5 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	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	14
β-strand	98-104	7	15
β-strand	114-122	9	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	155-162	8	15
β-strand	170-176	7	16
β-strand	184-189	6	16

Chain G: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	10
α-helix	311-313	3
α-helix	315-317	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, E	protein	181	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, F	protein	190	Homo sapiens	P01911 (AlphaFold model)
Hemagglutinin peptide	C, G	protein	13		P11133
superantigen	D, H	protein	216	Mycoplasma arthritidis	Q48898 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>1R5I_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, E)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B, F), FASTA

>1R5I_2 HLA class II histocompatibility antigen, DRB1-1 beta chain (chains B, F)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C, G), FASTA

>1R5I_3 Hemagglutinin peptide (chains C, G)
PKYVKQNTLKLAT

Sequence of entity 4 (D, H), FASTA

>1R5I_4 superantigen (chains D, H)
LGSMKLRVENPKKAQKHFVQNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYR
HAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADND
LSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELW
WFRSLLVKGVYLIKRYYEGDIELKTTSDFAKAVFED

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4

Primary citation

Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex. Zhao, Y., Li, Z., Drozd, S.J. et al. Structure (2004) 12:277-288. DOI 10.1016/S0969-2126(04)00020-6 · 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

Browse structure collections

About this viewer

MolViewer shows 1R5I directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.