7DV4: Anti-CTLA-4 VH domain

Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4. Determined by X-ray diffraction at 2.38 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 8
Atoms: 7,062
Mol. weight: 102.37 kDa
Released: 12 Jan 2022

Explore 7DV4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DV4 contains 22 α-helices and 93 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: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-41	9	2
β-strand	46-55	10	2
α-helix	59-60	2
β-strand	61-62	2	2
β-strand	68-72	5	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	112-116	5	2
α-helix	117	1

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	3
β-strand	12-13	2	4
β-strand	19-26	8	3
α-helix	30-32	3
β-strand	35-40	6	5
β-strand	47-52	6	5
β-strand	58-60	3	5
β-strand	68-73	6	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-98	7	5
β-strand	109-110	2	5
β-strand	114-116	3	5
β-strand	117-118	2	4

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-42	10	7
β-strand	45-55	11	7
α-helix	59-60	2
β-strand	61-62	2	7
β-strand	68-72	5	6
β-strand	76-81	6	6
β-strand	91-100	10	7
α-helix	104	1
β-strand	105-108	4	7
β-strand	112-116	5	7

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	8
β-strand	12	1	9
β-strand	18-26	9	8
α-helix	30-32	3
β-strand	35-40	6	10
β-strand	46-52	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-84	7	8
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	109-110	2	10
β-strand	114-116	3	10
β-strand	117	1	9

Chain E: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	11
β-strand	10-14	5	6
β-strand	17-25	9	11
β-strand	33-42	10	6
β-strand	45-55	11	6
β-strand	56	1	12
β-strand	58	1	12
α-helix	59-60	2
β-strand	61-62	2	6
β-strand	68-72	5	11
β-strand	76-84	9	11
α-helix	86-88	3
β-strand	90-100	11	6
α-helix	104	1
β-strand	105-108	4	6
β-strand	112-117	6	6

Chain F: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	13
β-strand	11-13	3	14
β-strand	19-26	8	13
α-helix	30-32	3
β-strand	35-40	6	14
β-strand	46-52	7	14
β-strand	58-60	3	14
α-helix	62-64	3
β-strand	65	1	13
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-98	7	14
β-strand	109-110	2	14
β-strand	114-118	5	14

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	15
β-strand	10-12	3	1
β-strand	19-24	6	15
β-strand	33-42	10	1
β-strand	45-55	11	1
α-helix	60	1
β-strand	61-62	2	1
β-strand	68-72	5	15
β-strand	76-81	6	15
α-helix	86-88	3
β-strand	90-100	11	1
α-helix	104	1
β-strand	105-108	4	1
β-strand	112-115	4	1

Chain H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	16
β-strand	11-13	3	17
β-strand	19-26	8	16
α-helix	30-32	3
β-strand	35-40	6	17
β-strand	46-52	7	17
β-strand	58-60	3	17
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-98	7	17
β-strand	109-110	2	17
β-strand	114-118	5	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytotoxic T-lymphocyte protein 4	A, C, E, G	protein	118	Homo sapiens	P16410 (AlphaFold model)
4003-1(VH)	B, D, F, H	protein	120	Homo sapiens

Sequence of entity 1 (A, C, E, G), FASTA

>7DV4_1 Cytotoxic T-lymphocyte protein 4 (chains A, C, E, G)
KAMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNEL
TFLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVID

Sequence of entity 2 (B, D, F, H), FASTA

>7DV4_2 4003-1(VH) (chains B, D, F, H)
GEVQLVESGGGLIQPGGSLRLSCAVSGFTVSKNYMSWVRQAPGKGLEWVSVVYSGGSKTY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARAVPHSPSSFDIWGQGTMVTVSS

Primary citation

An anti-CTLA-4 heavy chain-only antibody with enhanced T reg depletion shows excellent preclinical efficacy and safety profile. Gan, X., Shan, Q., Li, H. et al. Proc Natl Acad Sci U S A (2022) 119:e2200879119-e2200879119. DOI 10.1073/pnas.2200879119 · 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
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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