5KSV: HLA-DQ2.5-CLIP2

Crystal structure of HLA-DQ2.5-CLIP2. Determined by X-ray diffraction at 2.19 Å resolution. Released 5 Apr 2017.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,178
Mol. weight: 47.77 kDa
Released: 5 Apr 2017

Explore 5KSV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KSV contains 14 α-helices and 28 β-strands across 3 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-14	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
α-helix	56-76	21
α-helix	81-83	3
β-strand	88-93	6	2
β-strand	103-112	10	2
β-strand	118-123	6	3
β-strand	126-128	3	3
β-strand	132-134	3	2
α-helix	137	1
β-strand	138-139	2	2
β-strand	145-153	9	2
β-strand	161-166	6	3
β-strand	174-178	5	3

Chain B: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	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	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-88	8
α-helix	90-92	3
β-strand	95	1	4
α-helix	96-97	2
β-strand	98-103	6	5
β-strand	114-122	9	5
β-strand	123	1	4
β-strand	128-133	6	6
β-strand	136-138	3	6
β-strand	142-144	3	5
α-helix	145-147	3
β-strand	148-149	2	5
β-strand	155-162	8	5
α-helix	165-166	2
β-strand	170-176	7	6
β-strand	184-189	6	6

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II HLA-DQ-alpha chain	A	protein	199	Homo sapiens	P01909 (AlphaFold model)
MHC class II HLA-DQ-beta-1	B	protein	204	Homo sapiens	Q5Y7D3 (AlphaFold model)
HLA class II histocompatibility antigen gamma chain	C	protein	15	Homo sapiens	P04233 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5KSV_1 MHC class II HLA-DQ-alpha chain (chains A)
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQF
ALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVN
ITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHW
EPEIPAPMSELTEVDIEGR

Sequence of entity 2 (B), FASTA

>5KSV_2 MHC class II HLA-DQ-beta-1 (chains B)
RDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEY
WNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT
DFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL
QSPITVEWRAQSESAQSKVDIEGR

Sequence of entity 3 (C), FASTA

>5KSV_3 HLA class II histocompatibility antigen gamma chain (chains C)
MATPLLMQALPMGAL

Primary citation

Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides. Nguyen, T.B., Jayaraman, P., Bergseng, E. et al. J Biol Chem (2017) 292:9218-9228. DOI 10.1074/jbc.M117.785139 · PubMed

Other PDB entries of the same protein (UniProt P01909 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6U3M 1.9 Å, DQ2-P.fluor-alpha1a
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
6MFG 2.0 Å, HLA-DQ2-glia-alpha1
2NNA 2.1 Å, Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide
8W84 2.1 Å, HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02
9EJG 2.2 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
1S9V 2.22 Å, Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide
8W86 2.24 Å, HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02
1JK8 2.4 Å, Crystal structure of a human insulin peptide-HLA-DQ8 complex
6XP6 2.4 Å, 3C11-DQ2-glia-a2 complex
9EJH 2.45 Å, Peptide-independent T cell receptor recognition of HLA-DQ2
6MFF 2.6 Å, HLA-DQ2-glia-omega1

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