1ED3: Class I major histocompatibility antigen RT1-aa

Crystal structure of rat minor histocompatibility antigen complex RT1-aa/mtf-E. Determined by X-ray diffraction at 2.55 Å resolution. Released 28 Feb 2001.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 6,519
Mol. weight: 90.46 kDa
Released: 28 Feb 2001

Explore 1ED3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ED3 contains 27 α-helices and 60 β-strands across 5 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-12	11	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-104	11	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-223	2	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	257-263	7	4
β-strand	270-272	3	4

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
α-helix	14-15	2
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	13-14	2
α-helix	19-20	2
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	199-208	10	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	223	1	11
α-helix	225-227	3
β-strand	228-230	3	10
β-strand	234-235	2	10
β-strand	241-249	9	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	56	1	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Class I major histocompatibility antigen RT1-aa	A, D	protein	275	Rattus norvegicus	P16391 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Rattus norvegicus	P07151 (AlphaFold model)
Peptide mtf-E (13N3E)	C, F	protein	13		P05504 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1ED3_1 CLASS I MAJOR HISTOCOMPATIBILITY ANTIGEN RT1-AA (chains A, D)
GSHSLRYFYTAVSRPGLGEPRFIAVGYVDDTEFVRFDSDAENPRMEPRARWMEREGPEYW
EQQTRIAKEWEQIYRVDLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYRQDAYDG
RDYIALNEDLKTWTAADFAAQITRNKWERARYAERLRAYLEGTCVEWLSRYLELGKETLL
RSDPPEAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWE

Sequence of entity 2 (B, E), FASTA

>1ED3_2 BETA-2-MICROGLOBULIN (chains B, E)
IQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDW
SFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM

Sequence of entity 3 (C, F), FASTA

>1ED3_3 PEPTIDE MTF-E (13N3E) (chains C, F)
ILFPSSERLISNR

Primary citation

Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa. Speir, J.A., Stevens, J., Joly, E. et al. Immunity (2001) 14:81-92. DOI 10.1016/S1074-7613(01)00091-7 · PubMed

Other PDB entries of the same protein (UniProt P16391 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KJM 2.35 Å, TAP-A-associated rat MHC class I molecule
6NF7 2.9 Å, Crystal Structure of RT1.Aa-Bu31-10

Browse structure collections

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