5GGV: CTLA-4

CTLA-4 in complex with tremelimumab Fab. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,665
Mol. weight: 62.87 kDa
Released: 9 Nov 2016

Explore 5GGV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GGV contains 24 α-helices and 55 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 H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	58-60	3	8
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	8
β-strand	114-115	2	8
β-strand	119-123	5	8
β-strand	129	1	9
α-helix	130-131	2
β-strand	132-136	5	10
α-helix	140-142	3
β-strand	143-144	2	10
β-strand	147-157	11	10
β-strand	158	1	9
β-strand	163-166	4	11
α-helix	167-169	3
β-strand	171	1	11
β-strand	175-177	3	10
α-helix	178-180	3
β-strand	181-182	2	10
β-strand	188-197	10	10
α-helix	198-200	3
β-strand	207-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain L: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
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	62-66	5	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	93	1	3
α-helix	97	1
β-strand	98	1	2
α-helix	99	1
β-strand	102-106	5	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
α-helix	155	1
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-197	7	6
β-strand	205-210	6	6

Chain Y: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	12
β-strand	10-12	3	3
α-helix	13-14	2
β-strand	19-26	8	12
β-strand	33-42	10	3
β-strand	45-55	11	3
α-helix	58-60	3
β-strand	68-70	3	12
β-strand	76-81	6	12
α-helix	86-88	3
β-strand	90-100	11	3
α-helix	104	1
β-strand	105-108	4	3
β-strand	112-115	4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
light chain	L	protein	214	Homo sapiens
heavy chain	H	protein	239	Homo sapiens
Cytotoxic T-lymphocyte protein 4	Y	protein	126	Homo sapiens	P16410 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>5GGV_1 light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSINSYLDWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYYSTPFTFGPGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>5GGV_2 heavy chain (chains H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVIWYDGSNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDPRGATLYYYYYGMDVWGQGTT
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHH

Sequence of entity 3 (Y), FASTA

>5GGV_3 Cytotoxic T-lymphocyte protein 4 (chains Y)
KAMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNEL
TFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDPE
PCPDSD

Primary citation

Structural basis of checkpoint blockade by monoclonal antibodies in cancer immunotherapy. Lee, J.Y., Lee, H.T., Shin, W. et al. Nat Commun (2016) 7:13354-13354. DOI 10.1038/ncomms13354 · PubMed

Other PDB entries of the same protein (UniProt P16410 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CIO 1.1 Å, Molecular interactions of cytoplasmic region of CTLA-4 with SH2 domains of PI3-kinase
9DQ3 1.64 Å, Crystal structure of engineered Ipilimumab (mipi.4) Fab in complex with human CTLA-4
3OSK 1.8 Å, Crystal structure of human CTLA-4 apo homodimer
3BX7 2.1 Å, Engineered Human Lipocalin 2 (LCN2) in Complex with the Extracellular Domain of Human…
7ELX 2.14 Å, The crystal structure of CTLA-4 and Fab
7DV4 2.38 Å, Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4
7SU0 2.41 Å, Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.105 in complex with…
7SU1 2.53 Å, Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.106 in complex with…
2X44 2.6 Å, Structure of a strand-swapped dimeric form of CTLA-4
6RP8 2.6 Å, Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution
8GAB 2.72 Å, Crystal structure of CTLA-4 in complex with a high affinity CTLA-4 binder
1I8L 3.0 Å, Human B7-1/CTLA-4 co-stimulatory complex

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