3DMM: CD8 alpha beta/H-2Dd complex

Crystal structure of the CD8 alpha beta/H-2Dd complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 14 Jul 2009.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Mus musculus
Chains: 5
Atoms: 5,094
Mol. weight: 80.12 kDa
Released: 14 Jul 2009

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

Secondary structure: helices and β-sheets

3DMM contains 12 α-helices and 50 β-strands across 4 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	52-54	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	163-179	17
β-strand	183	1	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	229-230	2	3
α-helix	231-233	3
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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6-11	6	5
β-strand	21-30	10	5
β-strand	36-41	6	6
β-strand	44-45	2	6
α-helix	46	1
β-strand	50-51	2	5
β-strand	55-56	2	5
β-strand	62-70	9	5
β-strand	78-83	6	6
β-strand	91-94	4	6

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	7
β-strand	14	1	8
β-strand	22-29	8	7
β-strand	35-42	8	8
β-strand	51-57	7	8
β-strand	63-65	3	8
α-helix	67-69	3
β-strand	75-78	4	7
β-strand	84-89	6	7
β-strand	98-105	8	8
β-strand	110-112	3	8
β-strand	114	1	9
β-strand	116-118	3	8

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	10
β-strand	7-11	5	9
β-strand	16-21	6	10
β-strand	30-37	8	9
β-strand	44-52	9	9
β-strand	56-59	4	9
β-strand	69-72	4	10
β-strand	80-83	4	10
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	104-106	3	9
β-strand	110-115	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A	protein	275	Mus musculus	P01900 (AlphaFold model)
Beta-2 microglobulin	B	protein	100	Mus musculus	P01887 (AlphaFold model)
Synthetic peptide	P	protein	10
T-cell surface glycoprotein CD8 alpha chain	C	protein	166	Mus musculus	P01731 (AlphaFold model)
T-cell surface glycoprotein CD8 beta chain	D	protein	150	Mus musculus	P10300 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3DMM_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A)
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW
ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL
RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT
FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWG

Sequence of entity 2 (B), FASTA

>3DMM_2 Beta-2 microglobulin (chains B)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (P), FASTA

>3DMM_3 Synthetic peptide (chains P)
RGPGRAFVTI

Sequence of entity 4 (C), FASTA

>3DMM_4 T-cell surface glycoprotein CD8 alpha chain (chains C)
GSGEAKPQAPELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVY
MASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSV
VPVLQKVNSTTTKPVLRTPSPVHPTGTSQPQRPEDCRPRGSVKGTG

Sequence of entity 5 (D), FASTA

>3DMM_5 T-cell surface glycoprotein CD8 beta chain (chains D)
SSALIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGV
LYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDV
LPTTAPTKKTTLKMKKKKQCPFPHPETQKG

Primary citation

Structural basis of the CD8alphabeta/MHC class i interaction: focused recognition orients CD8beta to a T cell proximal position. Wang, R., Natarajan, K., Margulies, D.H. J Immunol (2009) 183:2554-2564. DOI 10.4049/jimmunol.0901276 · 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…

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