8S6Z: CD28

CD28 in complex with the antibody Fab fragment AI3. Determined by X-ray diffraction at 3.05 Å resolution. Released 18 Dec 2024.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,785
Mol. weight: 130.83 kDa
Ligands: NAG, ZN
Released: 18 Dec 2024

Explore 8S6Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S6Z contains 38 α-helices and 124 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.

Chains A and D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	99-102	4	2
β-strand	106-110	5	2
α-helix	113-115	3
β-strand	116	1	3
α-helix	117-118	2
β-strand	119-123	5	4
β-strand	130	1	4
β-strand	134-144	11	4
β-strand	145	1	3
β-strand	150-153	4	5
α-helix	154-156	3
β-strand	158	1	5
β-strand	162-164	3	4
α-helix	165-167	3
β-strand	168-169	2	4
β-strand	175-184	10	4
α-helix	185-190	6
β-strand	193-199	7	5
α-helix	200-202	3
β-strand	204-210	7	5

Chains B and E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	27C	1	8
β-strand	31	1	8
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-107	6	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	153-154	2	11
β-strand	159-160	2	10
β-strand	163	1	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-198	8	11
β-strand	205-210	6	11

Chain C: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	5-6	2	13
β-strand	10-13	4	14
β-strand	14	1	15
β-strand	17	1	15
β-strand	18-24	7	13
β-strand	32-39	8	14
β-strand	45-52	8	14
β-strand	58-62	5	14
β-strand	67-72	6	13
β-strand	76-82	7	13
α-helix	86-88	3
β-strand	90-100	11	14
α-helix	103-104	2
β-strand	105-106	2	14
β-strand	107	1	12
β-strand	113-117	5	14

Chain F: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
β-strand	5-6	2	28
β-strand	10-13	4	29
β-strand	14	1	30
β-strand	17	1	30
β-strand	18-24	7	28
β-strand	32-39	8	29
β-strand	45-52	8	29
β-strand	58-61	4	29
β-strand	67-72	6	28
β-strand	76-82	7	28
α-helix	86-88	3
β-strand	90-100	11	29
α-helix	103-104	2
β-strand	105-106	2	29
β-strand	107	1	27
β-strand	113-117	5	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain Fab fragment of AI3 antibody	A, D	protein	223	Homo sapiens
Light chain of AI3 antibody	B, E	protein	220	Homo sapiens
T-cell-specific surface glycoprotein CD28	C, F	protein	134	Homo sapiens	P10747 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8S6Z_1 Heavy chain Fab fragment of AI3 antibody (chains A, D)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKSYGAFDYWGQGTLVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 2 (B, E), FASTA

>8S6Z_2 Light chain of AI3 antibody (chains B, E)
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQNLRPPETFGQGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, F), FASTA

>8S6Z_3 T-cell-specific surface glycoprotein CD28 (chains C, F)
NKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQLQV
YSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKGK
HLCPSPLFPGPSKP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
ZN	Zinc ion	Zn	26

Water and common crystallization additives (GOL, IMD) are not listed.

Primary citation

NI-3201 Is a Bispecific Antibody Mediating PD-L1-Dependent CD28 Co-stimulation on T Cells for Enhanced Tumor Control. Majocchi, S., Lloveras, P., Nouveau, L. et al. Cancer Immunol Res (2025) 13:365-383. DOI 10.1158/2326-6066.CIR-24-0298 · PubMed

Other PDB entries of the same protein (UniProt P10747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GJI 0.9 Å, PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex
5AUL 1.1 Å, PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex
5GJH 1.2 Å, Gads SH2 domain/CD28-derived peptide complex
3WA4 1.35 Å, Grb2 SH2 domain/CD28-derived peptide complex
7PPN 1.9 Å, SHP2 catalytic domain in complex with CD28 (183-198) phosphopeptide (pTyr-191, p-Thr-195)
1YJD 2.7 Å, Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody…
6O8D 3.55 Å, Anti-CD28xCD3 CODV Fab bound to CD28
7VU5 Structure of the transmembrane domain of the CD28 dimer
8W2V Solution Structure of the CD28 hinge used in chimeric antigen receptor (CAR) T-cells

Browse structure collections

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