6RPJ: A Non-blocking anti-CTLA-4 Nanobody

A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4. Determined by X-ray diffraction at 3.25 Å resolution. Released 8 Jul 2020.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Homo sapiens, Camelus bactrianus
Chains: 8
Atoms: 7,424
Mol. weight: 118.42 kDa
Ligands: NAG
Released: 8 Jul 2020

Explore 6RPJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RPJ contains 27 α-helices and 108 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.

Chains A and C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	10-12	3	2
α-helix	13-14	2
β-strand	19-25	7	1
β-strand	33-41	9	2
β-strand	46-55	10	2
β-strand	61-62	2	2
β-strand	65	1	3
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	112-115	4	2

Chains B and D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	17-25	9	4
β-strand	34-39	6	6
α-helix	44-45	2
β-strand	46-51	6	6
β-strand	58-60	3	6
α-helix	62-64	3
β-strand	65	1	4
β-strand	68-72	5	4
β-strand	78-84	7	4
α-helix	88-90	3
β-strand	92-98	7	6
β-strand	103	1	2
β-strand	106	1	3
α-helix	110-112	3
β-strand	115-116	2	6
β-strand	120-122	3	6
β-strand	123-124	2	5

Chains E and G: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	13
β-strand	10-12	3	14
α-helix	13-14	2
β-strand	19-25	7	13
β-strand	33-41	9	14
β-strand	46-54	9	14
β-strand	61-62	2	14
β-strand	65	1	15
β-strand	68-72	5	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 F: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	11-12	2	17
β-strand	17-25	9	16
β-strand	34-39	6	18
β-strand	46-51	6	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	65	1	16
β-strand	68-72	5	16
β-strand	78-84	7	16
α-helix	88-90	3
β-strand	92-98	7	18
β-strand	103	1	14
β-strand	106	1	15
α-helix	110-112	3
β-strand	115-116	2	18
β-strand	120-122	3	18
β-strand	123-124	2	17

Chain H: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	12	1	23
β-strand	17-25	9	22
β-strand	34-39	6	24
α-helix	44-45	2
β-strand	46-51	6	24
β-strand	58-60	3	24
α-helix	62-64	3
β-strand	65	1	22
β-strand	68-72	5	22
β-strand	78-84	7	22
α-helix	88-90	3
β-strand	92-98	7	24
β-strand	103	1	20
β-strand	106	1	21
α-helix	110-112	3
β-strand	115-116	2	24
β-strand	120-122	3	24
β-strand	124	1	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytotoxic T-lymphocyte protein 4	A, C, E, G	protein	129	Homo sapiens	P16410 (AlphaFold model)
A non-blocking CTLA-4 nanobody	B, D, F, H	protein	142	Camelus bactrianus

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

>6RPJ_1 Cytotoxic T-lymphocyte protein 4 (chains A, C, E, G)
AMHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELT
FLDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDPEP
GGSHHHHHH

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

>6RPJ_2 A non-blocking CTLA-4 nanobody (chains B, D, F, H)
QVQLQESGGGSVQAGGSLTLSCAASGYANSNTCMGWFRQAPGKERERVAAISGVGTGTYY
ADSVKGRFTISRDNGKNTLFLQMNSLKPEDTAMYYCAAAPEGRAWCSRDPSGYNYWGQGT
QVTVSSGSMDPGGSHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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

Primary citation

A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4. Gao, H., Zhou, A. To be published.

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
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

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