1YJD: Human CD28

Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1). Determined by X-ray diffraction at 2.7 Å resolution. Released 15 Feb 2005.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 4,493
Mol. weight: 63.95 kDa
Ligands: NAG
Released: 15 Feb 2005

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

Secondary structure: helices and β-sheets

1YJD contains 14 α-helices and 59 β-strands across 3 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 C: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	11
β-strand	5-6	2	12
β-strand	10-12	3	13
β-strand	14	1	14
β-strand	17	1	14
β-strand	18-24	7	12
β-strand	32-39	8	13
β-strand	46-53	8	13
β-strand	59-61	3	13
β-strand	67-72	6	12
β-strand	76-82	7	12
α-helix	86-88	3
β-strand	90-100	11	13
β-strand	105-106	2	13
β-strand	107	1	11
β-strand	113-116	4	13

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-11	2	7
β-strand	18-20	3	6
β-strand	22-25	4	6
α-helix	29-31	3
β-strand	32-39	8	7
β-strand	45-52	8	7
β-strand	57-60	4	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
β-strand	92-100	9	7
β-strand	110	1	7
β-strand	114-117	4	7
β-strand	124	1	8
β-strand	127-131	5	9
β-strand	142-152	11	9
β-strand	153	1	8
β-strand	158-161	4	10
β-strand	166	1	10
β-strand	170-172	3	9
α-helix	173-175	3
β-strand	176-178	3	9
β-strand	181-191	11	9
β-strand	200-206	7	10
α-helix	207-209	3
β-strand	211-217	7	10

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-14	5	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
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-166	3
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	192-197	6	5
α-helix	204	1
β-strand	205-209	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment of 5.11A1 antibody light chain	L	protein	212	Mus musculus
Fab fragment of 5.11A1 antibody heavy chain	H	protein	222	Mus musculus
T-cell-specific surface glycoprotein CD28	C	protein	140	Homo sapiens	P10747 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1YJD_1 Fab fragment of 5.11A1 antibody light chain (chains L)
DIQMNQSPSSLSASLGDTITITCHASQNIYVWLNWYQQKPGNIPKLLIYKASNLHTGVPS
RFSGSGSGTGFTLTISSLQPEDIATYYCQQGQTYPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 2 (H), FASTA

>1YJD_2 Fab fragment of 5.11A1 antibody heavy chain (chains H)
QVQLQQSGPELVKPGTSVRISCEASGYTFTSYYIHWVKQRPGQGLEWIGCIYPGNVNTNY
NEKFKDKATLIVDTSSNTAYMQLSRMTSEDSAVYFCTRSHYGLDWNFDVWGAGTTVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (C), FASTA

>1YJD_3 T-cell-specific surface glycoprotein CD28 (chains C)
TGNKILVKQSPMLVAYDNAVNLSCKYSYNLFSREFRASLHKGLDSAVEVCVVYGNYSQQL
QVYSKTGFNCDGKLGNESVTFYLQNLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVK
GKHLCPSPLFPGPSKPLVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Crystal structure of a soluble CD28-Fab complex. Evans, E.J., Esnouf, R.M., Manso-Sancho, R. et al. Nat Immunol (2005) 6:271-279. DOI 10.1038/ni1170 · 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)
8S6Z 3.05 Å, CD28 in complex with the antibody Fab fragment AI3
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

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