3B9K: CD8alpha-beta

Crystal structure of CD8alpha-beta in complex with YTS 156.7 FAB. Determined by X-ray diffraction at 2.7 Å resolution. Released 11 Nov 2008.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: rattus rattus, Mus musculus
Chains: 8
Atoms: 10,298
Mol. weight: 150.82 kDa
Ligands: NAG
Released: 11 Nov 2008

Explore 3B9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B9K contains 34 α-helices and 132 β-strands across 8 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	12
β-strand	14-16	3	13
β-strand	22-29	8	12
β-strand	36-42	7	13
β-strand	51-56	6	13
β-strand	63-65	3	13
β-strand	75-80	6	12
β-strand	84-89	6	12
α-helix	94-96	3
β-strand	98-106	9	13
β-strand	109-112	4	13
α-helix	113-115	3
β-strand	116-120	5	13

Chains B and F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	14
β-strand	7-11	5	15
β-strand	16-21	6	14
α-helix	27-28	2
β-strand	30-37	8	15
β-strand	44-52	9	15
β-strand	57-59	3	15
β-strand	69-72	4	14
β-strand	80-83	4	14
α-helix	88-90	3
β-strand	92-99	8	15
β-strand	104-106	3	15
α-helix	107-109	3
β-strand	110-115	6	15

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	85-90	6	17
β-strand	97-98	2	17
β-strand	102-106	5	17
β-strand	111	1	18
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-154	2	20
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-186	4
β-strand	192-198	7	20
β-strand	201-208	8	20
α-helix	211-213	3

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
β-strand	18-25	8	21
β-strand	34-39	6	23
β-strand	46-51	6	23
β-strand	57-59	3	23
α-helix	64-66	3
β-strand	67-72	6	21
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-94	7	23
β-strand	102-103	2	23
β-strand	107-109	3	23
β-strand	110-111	2	22
β-strand	117	1	24
β-strand	120-124	5	25
β-strand	138-147	10	25
β-strand	148	1	24
β-strand	153-157	4	26
α-helix	160-162	3
β-strand	172-173	2	25
α-helix	174-176	3
β-strand	177-178	2	25
β-strand	187-195	9	25
α-helix	198-201	3
β-strand	206-212	6	26
β-strand	217-222	6	26

Chain E: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	27
β-strand	14-16	3	28
β-strand	22-29	8	27
β-strand	36-42	7	28
β-strand	51-56	6	28
β-strand	63-65	3	28
α-helix	67-70	4
β-strand	75-80	6	27
β-strand	84-89	6	27
β-strand	98-106	9	28
β-strand	109-112	4	28
β-strand	113	1	27
α-helix	114-115	2
β-strand	116-120	5	28

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	64-66	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	102-103	2	8
β-strand	107-109	3	8
β-strand	110-111	2	7
α-helix	114-116	3
β-strand	117	1	9
β-strand	120-124	5	10
β-strand	138-147	10	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	160-162	3
β-strand	164	1	11
β-strand	172-173	2	10
β-strand	177-178	2	10
β-strand	187-195	9	10
β-strand	206-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11
α-helix	223-229	2

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	154	1	5
β-strand	159-163	5	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	192-197	6	5
β-strand	205-207	3	5
α-helix	211-213	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab Light Chain	C, L	protein	213	rattus rattus	P01836 (AlphaFold model)
Fab Heavy chain	D, H	protein	214	rattus rattus	P20761 (AlphaFold model)
T-cell surface glycoprotein CD8 alpha chain	A, E	protein	131	Mus musculus	P01731 (AlphaFold model)
T-cell surface glycoprotein CD8 beta chain	B, F	protein	125	Mus musculus	P10300 (AlphaFold model)

Sequence of entity 1 (C, L), FASTA

>3B9K_1 Fab Light Chain (chains C, L)
DIKMTQSPASLSASLGDKVTITCQASQNIDKYIAWYQQKPGKAPRQLIHYTSTLVSGTPS
RFSGSGSGRDYTFSISSVESEDIASYYCLQYDTLYTFGAGTKLELKRADAAPTVSIFPPS
MEQLTSGGATVVCFVNNFYPRDISVKWKIDGSEQRDGVLDSVTDQDSKDSTYSMSSTLSL
TKVEYERHNLYTCEVVHKTSSSPVVKSFNRGEC

Sequence of entity 2 (D, H), FASTA

>3B9K_2 Fab Heavy chain (chains D, H)
QVRLQESGPGLVQPSQTLSLTCSVSGFSLISDSVHWVRQPPGKGLEWMGGIWADGSTEYN
SALKSRLSISRDTSKSQGFLKMNSLQTDDTAIYFCTSNRESYYFDYWGQGTMVTVSSAQT
TAPSVYPLAPGCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGALSSDVHTFPAVLQSGLYT
LTSSVTSSTWPSQTVTCNVAHPASSTKVDKAVEA

Sequence of entity 3 (A, E), FASTA

>3B9K_3 T-cell surface glycoprotein CD8 alpha chain (chains A, E)
KPQAPELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSH
NKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQ
KVNSSADLVPR

Sequence of entity 4 (B, F), FASTA

>3B9K_4 T-cell surface glycoprotein CD8 beta chain (chains B, F)
LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYG
ESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDVSSA
DLVPR

Ligands and cofactors

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

Primary citation

The Crystal Structure of CD8 in Complex with YTS156.7.7 Fab and Interaction with Other CD8 Antibodies Define the Binding Mode of CD8 alphabeta to MHC Class I. Shore, D.A., Issafras, H., Landais, E. et al. J Mol Biol (2008) 384:1190-1202. DOI 10.1016/j.jmb.2008.09.069 · PubMed

Other PDB entries of the same protein (UniProt P01836 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ARJ 2.88 Å, CD8alpha-alpha in complex with YTS 105.18 Fab

Browse structure collections

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