6XY2: CTLA-4

Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody. Determined by X-ray diffraction at 3.05 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,163
Mol. weight: 63.5 kDa
Ligands: NAG
Released: 9 Dec 2020

Explore 6XY2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XY2 contains 16 α-helices and 58 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 A: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	33-42	10	2
β-strand	45-55	11	2
β-strand	60-62	3	2
α-helix	63	1
β-strand	68-69	2	1
β-strand	72	1	1
β-strand	76-82	7	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 H: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	11-12	2	4
β-strand	18-19	2	5
β-strand	21-25	5	3
β-strand	33-39	7	2
β-strand	46-52	7	2
β-strand	70-72	3	3
β-strand	77-79	3	3
β-strand	81-82	2	5
α-helix	87-89	3
β-strand	91-103	13	2
β-strand	106-115	10	2
β-strand	119-121	3	2
β-strand	122-123	2	4
α-helix	127-128	2
β-strand	129	1	6
α-helix	130-131	2
β-strand	132-136	5	7
β-strand	148-157	10	7
β-strand	158	1	6
β-strand	163-166	4	8
β-strand	175-177	3	7
α-helix	178-180	3
β-strand	181-182	2	7
β-strand	188-196	9	7
β-strand	207-212	6	8
β-strand	217-222	6	8

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-12	3	10
β-strand	19	1	9
β-strand	22-25	4	9
β-strand	33-38	6	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-90	6	10
α-helix	97	1
β-strand	98	1	10
α-helix	99	1
β-strand	102-105	4	10
β-strand	111	1	11
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	144-150	7	13
β-strand	154-155	2	13
β-strand	159-160	2	12
β-strand	163-164	2	12
α-helix	165-167	3
β-strand	173-182	10	12
α-helix	183-186	4
β-strand	191-198	8	13
α-helix	204	1
β-strand	205-210	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytotoxic T-lymphocyte protein 4	A	protein	123	Homo sapiens	P16410 (AlphaFold model)
Heavy chain	H	protein	247	Homo sapiens
Light chain	L	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>6XY2_1 Cytotoxic T-lymphocyte protein 4 (chains A)
MHVAQPAVVLASSRGIASFVCEYASPGKATEVRVTVLRQADSQVTEVCAATYMMGNELTF
LDDSICTGTSSGNQVNLTIQGLRAMDTGLYICKVELMYPPPYYLGIGNGTQIYVIDPEPC
PDS

Sequence of entity 2 (H), FASTA

>6XY2_2 Heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGFSLTSYGLSWIRQPPGKGLEWIGYIWYDGNTNFH
SPLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCAKTEGHYYGSNYGYYALDYWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTMDPGGSH
HHHHHHH

Sequence of entity 3 (L), FASTA

>6XY2_3 Light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASENIYSNLAWYQQKQGKAPKLLLYAATNLQDGVPS
RFSGSGSGTDYTLTISSLQPEDFATYFCQHLWGTPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structure of CTLA-4 complexed with a pH-sensitive cancer immunotherapeutic antibody. Gao, H., Cai, H., Liu, J. et al. Cell Discov (2020) 6:79-79. DOI 10.1038/s41421-020-00202-9 · 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
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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