8VSP: Human invariant chain

Cryo-EM structure of human invariant chain in complex with HLA-DQ. Determined by electron microscopy at 3.12 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 3.12 Å
Organism: Homo sapiens
Chains: 9
Atoms: 11,388
Mol. weight: 301.56 kDa
Ligands: NAG
Released: 8 May 2024

Explore 8VSP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VSP contains 33 α-helices and 87 β-strands across 9 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, D and G: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	1
β-strand	22-29	8	1
β-strand	32-38	7	1
β-strand	43-46	4	1
α-helix	49-51	3
β-strand	55	1	2
α-helix	58-78	21
β-strand	90-95	6	3
β-strand	105-114	10	3
β-strand	120-125	6	4
β-strand	128-130	3	4
β-strand	134-136	3	3
β-strand	140-141	2	3
β-strand	147-155	9	3
β-strand	163-168	6	4
β-strand	176-180	5	4
α-helix	189-220	32

Chains B, E and H: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	23-32	10	1
β-strand	36-41	6	1
β-strand	48-49	2	1
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-88	8
β-strand	95	1	5
β-strand	98-102	5	6
β-strand	115-122	8	6
β-strand	123	1	5
β-strand	128-133	6	7
β-strand	137	1	7
β-strand	142-149	8	6
β-strand	155-161	7	6
β-strand	171-176	6	7
β-strand	184-188	5	7
α-helix	197-224	28

Chains C, F and I: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	49-95	47
α-helix	100-104	5
β-strand	106	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DQ alpha 1 chain	A, D, G	protein	288	Homo sapiens	P01909 (AlphaFold model)
HLA class II histocompatibility antigen, DQ beta 1 chain	B, E, H	protein	295	Homo sapiens	P01920 (AlphaFold model)
HLA class II histocompatibility antigen gamma chain	C, F, I	protein	308	Homo sapiens	P04233 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>8VSP_1 HLA class II histocompatibility antigen, DQ alpha 1 chain (chains A, D, G)
MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV
DLGRKETVWCLPVLRQFRFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKS
PVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLP
SAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFIIR
GLRSVGASRHQGPLAAALEVLFQGPGAAEDQVDPRLIDGKHHHHHHHH

Sequence of entity 2 (B, E, H), FASTA

>8VSP_2 HLA class II histocompatibility antigen, DQ beta 1 chain (chains B, E, H)
MSWKKALRIPGGLRAATVTLMLAMLSTPVAEGRDSPEDFVYQFKAMCYFTNGTERVRYVT
RYIYNREEYARFDSDVEVYRAVTPLGPPDAEYWNSQKEVLERTRAELDTVCRHNYQLELR
TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLI
RNGDWTFQILVMLEMTPQHGDVYTCHVEHPSLQNPITVEWRAQSESAQSKMLSGIGGFVL
GLIFLGLGLIIHHRSQKGLLHAAALEVLFQGPGAAEDQVDPRLIDGKHHHHHHHH

Sequence of entity 3 (C, F, I), FASTA

>8VSP_3 HLA class II histocompatibility antigen gamma chain (chains C, F, I)
MDYKDDDDAGTSRHRRRSRSCREDQKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGA
LYTGFSILVTLLLAGQATTAYFLYQQQGRLDKLTVTSQNLQLENLRMKLPKPPKPVSKMR
MATPLLMQALPMGALPQGPMQNATKYGNMTEDHVMHLLQNADPLKVYPPLKGSFPENLRH
LKNTMETIDWKVFESWMHHWLLFEMSRHSLEQKPTDAPPKVLTKCQEEVSHIPAVHPGSF
RPKCDENGNYLPLQCYGSIGYCWCVFPNGTEVPNTRSRGHHNCSESLELEDPSSGLGVTK
QDLGPVPM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Structural insights into human MHC-II association with invariant chain. Wang, N., Waghray, D., Caveney, N.A. et al. Proc Natl Acad Sci U S A (2024) 121:e2403031121-e2403031121. DOI 10.1073/pnas.2403031121 · 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
5KSV 2.19 Å, Crystal structure of HLA-DQ2.5-CLIP2
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

Browse structure collections

About this viewer

MolViewer shows 8VSP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.