6HBY: PDB entry 6HBY

HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope. Determined by X-ray diffraction at 1.95 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,784
Mol. weight: 92.17 kDa
Ligands: PO4
Released: 14 Aug 2019

Explore 6HBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HBY contains 29 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.

Chain A: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	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	126-128	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	161-166	6	5
β-strand	174-178	5	5

Chains B and E: 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	65-74	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	98-104	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: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5	1
β-strand	6	1	2
α-helix	7-15	9

Chain D: 5 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	46-50	5
β-strand	53	1	10
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	11
α-helix	86-87	2
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
α-helix	137	1
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 F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5	1
β-strand	6	1	10
α-helix	7	1
α-helix	9-15	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	178	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, E	protein	191	Homo sapiens	P01911 (AlphaFold model)
ARRPPLAELAALNLSGSRL 5T4 tumour epitope	C, F	protein	19	Homo sapiens	Q13641 (AlphaFold model)
HLA class II histocompatibility antigen, DR alpha chain	D	protein	180	Homo sapiens	P01903 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6HBY_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALAN
IAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWL
RNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF

Sequence of entity 2 (B, E), FASTA

>6HBY_2 HLA class II histocompatibility antigen, DRB1-1 beta chain (chains B, E)
MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAE
YWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSV
SGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPS
VTSPLTVEWRA

Sequence of entity 3 (C, F), FASTA

>6HBY_3 ARRPPLAELAALNLSGSRL 5T4 tumour epitope (chains C, F)
ARRPPLAELAALNLSGSRL

Sequence of entity 4 (D), FASTA

>6HBY_4 HLA class II histocompatibility antigen, DR alpha chain (chains D)
KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALA
NIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTW
LRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	5

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

Primary citation

Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope. MacLachlan, B.J., Dolton, G., Papakyriakou, A. et al. J Biol Chem (2019) 294:20246-20258. DOI 10.1074/jbc.RA119.009437 · 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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