6ATF: HLA-DRB1*1402

HLA-DRB1*1402 in complex with Vimentin59-71. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 Sept 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 7,456
Mol. weight: 94.89 kDa
Ligands: NAG
Released: 13 Sept 2017

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

Secondary structure: helices and β-sheets

6ATF contains 32 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	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	126-128	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: 9 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
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
α-helix	147	1
β-strand	148-149	2	7
β-strand	155-162	8	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chains C and F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2
α-helix	3-5	3
α-helix	10-12	3

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	160-166	7	13
β-strand	174-179	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, D	protein	189	Homo sapiens	P01903 (AlphaFold model)
MHC class II antigen	B, E	protein	200	Homo sapiens	A0A0A1I7H6 (AlphaFold model)
Vimentin59-71	C, F	protein	13	synthetic construct	P08670 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6ATF_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DTSGDDDDK

Sequence of entity 2 (B, E), FASTA

>6ATF_2 MHC class II antigen (chains B, E)
GSGDTRPRFLEYSTSECHFFNGTERVRFLERYFHNQEENVRFDSDVGEYRAVTELGRPDA
EYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVHPKVTVYPSKTQPLQHHNLLVCS
VSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHP
SVTSPLTVEWRATGGDDDDK

Sequence of entity 3 (C, F), FASTA

>6ATF_3 Vimentin59-71 (chains C, F)
GVYATRSSAVRLR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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

Primary citation

Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis. Scally, S.W., Law, S.C., Ting, Y.T. et al. Ann Rheum Dis (2017) 76:1915-1923. DOI 10.1136/annrheumdis-2017-211300 · 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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