7SU0: Acidic pH-selective Ipilimumab variant Ipi.105

Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.105 in complex with CTLA-4. Determined by X-ray diffraction at 2.41 Å resolution. Released 2 Mar 2022.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,347
Mol. weight: 124.62 kDa
Ligands: NAG, FLC
Released: 2 Mar 2022

Explore 7SU0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SU0 contains 38 α-helices and 110 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.

Chain C: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-12	3	2
α-helix	13-14	2
β-strand	19-26	8	1
β-strand	33-42	10	2
β-strand	45-55	11	2
β-strand	68-73	6	1
β-strand	76-81	6	1
α-helix	86-88	3
β-strand	90-100	11	2
α-helix	104	1
β-strand	105-108	4	2
β-strand	112-115	4	2

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
β-strand	10-12	3	14
α-helix	13-14	2
β-strand	19-26	8	13
β-strand	33-42	10	14
β-strand	45-55	11	14
β-strand	56	1	15
β-strand	58	1	15
β-strand	68-73	6	13
β-strand	76-81	6	13
α-helix	86-88	3
β-strand	90-100	11	14
α-helix	104	1
β-strand	105-108	4	14
β-strand	112-115	4	14

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	10-12	3	4
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	46-51	6	4
β-strand	57-59	3	4
α-helix	61-63	3
β-strand	67-72	6	3
β-strand	77-82	6	3
α-helix	84-86	3
β-strand	88-95	8	4
β-strand	100A-103	4	4
β-strand	107-111	5	4
β-strand	117	1	5
α-helix	118-119	2
β-strand	120-124	5	6
β-strand	136-145	10	6
β-strand	146	1	5
β-strand	150-154	5	7
α-helix	155-157	3
β-strand	159	1	7
β-strand	163-165	3	6
α-helix	166-168	3
β-strand	169-170	2	6
β-strand	176-184	9	6
α-helix	186-189	4
β-strand	194-200	7	7
β-strand	205-211	7	7

Chain I: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	57-59	3	17
α-helix	61-63	3
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-95	8	17
β-strand	100A-103	4	17
β-strand	107-111	5	17
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
β-strand	136-145	10	19
β-strand	146	1	18
β-strand	151-154	4	20
α-helix	155-157	3
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-184	9	19
α-helix	187-189	3
β-strand	194-200	7	20
β-strand	205-211	7	20

Chain L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	93	1	2
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	144-150	7	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-198	8	12
β-strand	205-210	6	12

Chain M: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-90	7	22
β-strand	93	1	14
α-helix	96	1
β-strand	97-98	2	22
β-strand	102-106	5	22
β-strand	111	1	23
α-helix	112-113	2
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	145-150	6	25
β-strand	153-154	2	25
α-helix	155	1
β-strand	159-163	5	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-187	5
β-strand	192-197	6	25
β-strand	205-209	5	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytotoxic T-lymphocyte protein 4	C, D	protein	125	Homo sapiens	P16410 (AlphaFold model)
Fab heavy chain	H, I	protein	229	Homo sapiens
Fab light chain	L, M	protein	215	Homo sapiens

Sequence of entity 1 (C, D), FASTA

>7SU0_1 Cytotoxic T-lymphocyte protein 4 (chains C, D)
KAMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNEL
TFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDGH
HHHHH

Sequence of entity 2 (H, I), FASTA

>7SU0_2 Fab heavy chain (chains H, I)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSHYTMHWVRQAPGKGLEWVTFISYDGHNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGGHHHHHH

Sequence of entity 3 (L, M), FASTA

>7SU0_3 Fab light chain (chains L, M)
EIVLTQSPGTLSLSPGERATLSCRASQEVGESELAWYQQKPGQAPRLLIYGAFSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
FLC	Citrate anion	C6 H5 O7	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Improved therapeutic index of an acidic pH-selective antibody. Lee, P.S., MacDonald, K.G., Massi, E. et al. MAbs (2022) 14:2024642-2024642. DOI 10.1080/19420862.2021.2024642 · 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
5GGV 2.0 Å, CTLA-4 in complex with tremelimumab Fab
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
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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