6H6H: H-2D cell surface glycoprotein

Crystal structures of the murine class I major histocompatibility complex H-2Dbm13 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: 6,551
Mol. weight: 103.96 kDa
Released: 14 Aug 2019

Explore 6H6H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H6H contains 25 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: 9 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	138-150	13
α-helix	152-161	10
α-helix	163-175	13
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
α-helix	231-233	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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	9
β-strand	6-11	6	10
β-strand	21-30	10	10
β-strand	31	1	9
β-strand	36-41	6	11
β-strand	44-45	2	11
α-helix	46	1
β-strand	50-51	2	10
α-helix	52-54	3
β-strand	55-56	2	10
β-strand	62-70	9	10
β-strand	78-83	6	11
β-strand	91-94	4	11

Chains C and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2

Chain D: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	5
α-helix	18-20	3
β-strand	21-28	8	5
β-strand	31-37	7	5
β-strand	46-47	2	5
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	5
β-strand	109-118	10	5
β-strand	121-126	6	5
β-strand	133-135	3	5
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-175	12
β-strand	183	1	6
α-helix	184-185	2
β-strand	186-193	8	7
β-strand	198-208	11	7
β-strand	209	1	6
β-strand	214-219	6	8
β-strand	222-223	2	8
β-strand	229-230	2	7
α-helix	231-233	3
β-strand	234-235	2	7
β-strand	241-250	10	7
α-helix	254-256	3
β-strand	257-262	6	8
β-strand	270-272	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2D cell surface glycoprotein	A, D	protein	338	Mus musculus	Q31167 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Mus musculus	P01887 (AlphaFold model)
Ser-gly-pro-ser-asn-thr-pro-pro-glu-ile	C, F	protein	10	unidentified adenovirus	P03255 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6H6H_1 H-2D cell surface glycoprotein (chains A, D)
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW
ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYQQYAYDG
RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL
RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT
FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPPSTDSYMVIVAVLGVLGAMAIIG
AVVAFVMKRRRNTGGKGGDYALAPGSQSSEMSLRDCKA

Sequence of entity 2 (B, E), FASTA

>6H6H_2 Beta-2-microglobulin (chains B, E)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F), FASTA

>6H6H_3 SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE (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. Abualrous, E.T., Han, X., Badia-Martines, D. et al. To be published.

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