1BQH: Murine CD8AA ectodomain fragment

Murine CD8AA ectodomain fragment in complex with H-2KB/VSV8. Determined by X-ray diffraction at 2.8 Å resolution. Released 19 Aug 1998.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 10
Atoms: 10,204
Mol. weight: 147.55 kDa
Ligands: NAG
Released: 19 Aug 1998

Explore 1BQH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BQH contains 26 α-helices and 103 β-strands across 10 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
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	138-148	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-180	16
β-strand	183	1	2
β-strand	186-194	9	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	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	253-256	4
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6	1	6
β-strand	9-11	3	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	51	1	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	92-94	3	7
α-helix	95	1

Chains C and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain D: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	45-47	3	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-102	9	8
β-strand	111-118	8	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-148	11
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-179	16
β-strand	183	1	9
β-strand	186-194	9	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	213-219	7	11
β-strand	222-223	2	11
β-strand	228-230	3	10
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-263	7	11
β-strand	270-272	3	11

Chain E: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6	1	12
β-strand	9-11	3	13
β-strand	21-30	10	13
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain G: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	15
β-strand	22-29	8	15
β-strand	36-41	6	16
β-strand	51-56	6	16
β-strand	63-65	3	16
β-strand	75-80	6	15
β-strand	84-89	6	15
α-helix	94-96	3
β-strand	99-105	7	16
β-strand	110-112	3	16
β-strand	116-117	2	16

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	17
β-strand	14-16	3	18
β-strand	22-29	8	17
β-strand	36-42	7	18
β-strand	50-56	7	18
β-strand	63-65	3	18
α-helix	68-70	3
β-strand	75-79	5	17
β-strand	84-89	6	17
β-strand	98-106	9	18
β-strand	109-112	4	18
α-helix	113-115	3
β-strand	116-120	5	18

Chain I: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	19
β-strand	14-16	3	20
β-strand	22-29	8	19
β-strand	36-42	7	21
β-strand	51-56	6	21
β-strand	63-65	3	21
α-helix	67-69	3
β-strand	75-80	6	19
β-strand	84-89	6	19
β-strand	98-106	9	21
β-strand	109-112	4	21
β-strand	116-117	2	21
β-strand	118-120	3	20

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (H-2 class I histocompatibility antigen)	A, D	protein	274	Mus musculus	P01901 (AlphaFold model)
Protein (beta-2-microglobulin )	B, E	protein	99	Mus musculus	P01887 (AlphaFold model)
Protein (VSV8)	C, F	protein	8
Protein (CD8A or LYT2 or lyt-2)	G, H, I, K	protein	129	Mus musculus	P01731 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>1BQH_1 PROTEIN (H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN) (chains A, D)
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW
ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG
CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL
RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW

Sequence of entity 2 (B, E), FASTA

>1BQH_2 PROTEIN (BETA-2-MICROGLOBULIN ) (chains B, E)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, F), FASTA

>1BQH_3 PROTEIN (VSV8) (chains C, F)
RGYVYQGL

Sequence of entity 4 (G, H, I, K), FASTA

>1BQH_4 PROTEIN (CD8A OR LYT2 OR LYT-2) (chains G, H, I, K)
KPQAPELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSH
NKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQ
KVSSADLVP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural basis of CD8 coreceptor function revealed by crystallographic analysis of a murine CD8alphaalpha ectodomain fragment in complex with H-2Kb. Kern, P.S., Teng, M.K., Smolyar, A. et al. Immunity (1998) 9:519-530. DOI 10.1016/S1074-7613(00)80635-4 · PubMed

Other PDB entries of the same protein (UniProt P01901 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LK2 1.35 Å, 1.35A crystal structure of H-2Kb complexed with the GNYSFYAL peptide
1G7P 1.5 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
1KPU 1.5 Å, High resolution crystal structure of the MHC class I complex H-2Kb/VSV8
1G7Q 1.6 Å, Crystal structure of MHC class I H-2KB heavy chain complexed with beta-2 microglobulin…
3TID 1.65 Å, Crystal structure of the LCMV derived peptide GP34 in complex with the murine mhc class…
1FZK 1.7 Å, MHC class I natural mutant H-2KBM1 heavy chain complexed with beta-2 microglobulin and…
1KPV 1.71 Å, High resolution crystal structure of the MHC class I complex H-2Kb/SEV9
1LEG 1.75 Å, Crystal Structure of H-2Kb bound to the dEV8 peptide
6GB6 1.78 Å, Structure of H-2Kb with dipeptide GL
1FZM 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1FZO 1.8 Å, MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and…
1T0N 1.8 Å, Conformational switch in polymorphic H-2K molecules containing an HSV peptide

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