6H6D: PDB entry 6H6D

Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with adenovirus-derived peptide Ad10. Determined by X-ray diffraction at 2.4 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Mus musculus, unidentified adenovirus
Chains: 6
Atoms: 6,479
Mol. weight: 103.81 kDa
Released: 14 Aug 2019

Explore 6H6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H6D contains 20 α-helices and 60 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
α-helix	18-20	3
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
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	139-150	12
α-helix	152-161	10
α-helix	163-174	12
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chains B and E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
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

Chains C and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2

Chain D: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	8
α-helix	18-20	3
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	139-150	12
α-helix	152-161	10
α-helix	163-175	13
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
β-strand	229-230	2	10
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A, D	protein	338	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Mus musculus	P01887 (AlphaFold model)
Early E1A protein	C, F	protein	10	unidentified adenovirus	P03255 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6H6D_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, D)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPPSTDSYMVIVAVLGVLGAMAIIG
AVVAFVMKRRRNTGGKGGDYALAPGSQSSEMSLRDCKA

Sequence of entity 2 (B, E), FASTA

>6H6D_2 Beta-2-microglobulin (chains B, E)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F), FASTA

>6H6D_3 Early E1A protein (chains C, F)
SGPSNTPPEI

Primary citation

Crystal structures of H-2Db and H-2Dbm13 with cancer-associated Ad 10 peptide reveal that subtle changes in the peptide environment impact thermostability and alloreactivity. Han, X., Abualrous, E.T., Badia-Martines, D. et al. To be published.

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…

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