3E6F: MHC CLASS I H-2Dd Heavy chain

MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PA9, from the Human immunodeficiency virus (BaL) envelope glycoprotein 120. Determined by X-ray diffraction at 2.41 Å resolution. Released 18 Aug 2009.

Method: X-ray diffraction
Resolution: 2.41 Å
Organisms: Mus musculus, Human immunodeficiency virus 1
Chains: 3
Atoms: 3,256
Mol. weight: 44.58 kDa
Released: 18 Aug 2009

Explore 3E6F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3E6F contains 11 α-helices and 30 β-strands across 2 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	3
α-helix	232-233	2
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A	protein	274	Mus musculus	P01900 (AlphaFold model)
Beta-2 microglobulin	B	protein	99	Mus musculus	P01887 (AlphaFold model)
Envelope glycoprotein 9-residue peptide	P	protein	9	Human immunodeficiency virus 1	P05878

Sequence of entity 1 (A), FASTA

>3E6F_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A)
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW
ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL
RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT
FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRW

Sequence of entity 2 (B), FASTA

>3E6F_2 BETA-2 MICROGLOBULIN (chains B)
MQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (P), FASTA

>3E6F_3 Envelope glycoprotein 9-residue peptide (chains P)
IGPGRAFYA

Primary citation

Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity. Honda, M., Wang, R., Kong, W.P. et al. J Immunol (2009) 183:2425-2434. DOI 10.4049/jimmunol.0900581 · PubMed

Other PDB entries of the same protein (UniProt P01900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…
8FHU 1.8 Å, Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by…
5T7G 1.96 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
3E6H 2.1 Å, MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…
5IVX 2.1 Å, Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex
8FHL 2.19 Å, Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented…
1QO3 2.3 Å, Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
8D5F 2.31 Å, The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
5KD7 2.35 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
6NPR 2.37 Å, Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide…
1BII 2.4 Å, The crystal structure of H-2DD MHC class I in complex with the HIV-1 derived peptide…

Browse structure collections

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