1FV1: Major histocompatibility complex alpha chain

Structural basis for the binding of an immunodominant peptide from myelin basic protein in different registers by two HLA-DR2 alleles. Determined by X-ray diffraction at 1.9 Å resolution. Released 27 Sept 2000.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,795
Mol. weight: 91.66 kDa
Released: 27 Sept 2000

Explore 1FV1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1FV1 contains 26 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.

Chains A and D: 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	53	1	2
α-helix	56-76	21
α-helix	80-84	5
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	126-127	2	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: 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	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
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	137	1	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

Chains C and F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	91	1	2
α-helix	95-102	8

Chain E: 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	55-62	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	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	137	1	16
β-strand	142-144	3	15
β-strand	148-149	2	15
β-strand	155-163	9	15
β-strand	171-176	6	16
β-strand	184-188	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major histocompatibility complex alpha chain	A, D	protein	181	Homo sapiens	P01903 (AlphaFold model)
Major histocompatibility complex beta chain	B, E	protein	190	Homo sapiens	Q30154 (AlphaFold model)
Myelin basic protein	C, F	protein	20		P02686 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1FV1_1 MAJOR HISTOCOMPATIBILITY COMPLEX ALPHA CHAIN (chains A, D)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B, E), FASTA

>1FV1_2 MAJOR HISTOCOMPATIBILITY COMPLEX BETA CHAIN (chains B, E)
GDTRPRFLQQDKYECHFFNGTERVRFLHRDIYNQEEDLRFDSDVGEYRAVTELGRPDAEY
WNSQKDFLEDRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPARTQTLQHHNLLVCSVN
GFYPGSIEVRWFRNSQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C, F), FASTA

>1FV1_3 MYELIN BASIC PROTEIN (chains C, F)
NPVVHFFKNIVTPRTPPPSQ

Primary citation

Structural basis for the binding of an immunodominant peptide from myelin basic protein in different registers by two HLA-DR2 proteins. Li, Y., Li, H., Martin, R. et al. J Mol Biol (2000) 304:177-188. DOI 10.1006/jmbi.2000.4198 · 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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