8ARI: C-terminal-binding protein 1

Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament. Determined by electron microscopy at 3.0 Å resolution. Released 23 Aug 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 34
Atoms: 63,756
Mol. weight: 1347.06 kDa
Ligands: NAD
Released: 23 Aug 2023

Explore 8ARI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ARI contains 360 α-helices and 428 β-strands across 34 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, b, c, d, e, f, g, h, i and j: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	317-318	2	1
β-strand	343-344	2	25

Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W and X: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	1
β-strand	50-53	4	1
α-helix	59-61	3
α-helix	64-68	5
β-strand	72-75	4	1
β-strand	81	1	2
α-helix	83-87	5
β-strand	94-97	4	1
β-strand	105	1	2
α-helix	107-113	7
β-strand	116-119	4	1
α-helix	125-140	16
α-helix	144-151	8
α-helix	159-165	7
β-strand	176-180	5	3
α-helix	184-193	10
α-helix	194-196	3
β-strand	199-203	5	3
α-helix	211-215	5
β-strand	218-219	2	3
α-helix	223-228	6
β-strand	232-235	4	3
β-strand	247	1	4
α-helix	249-252	4
β-strand	259-263	5	3
α-helix	267-269	3
β-strand	270	1	4
α-helix	272-281	10
β-strand	284-289	6	3
β-strand	310-312	3	3
α-helix	321-339	19
β-strand	350	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-terminal-binding protein 1	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	protein	457	Homo sapiens	Q13363 (AlphaFold model)
Retinoic acid-induced protein 2	a, b, c, d, e, f, g, h, i, j	protein	129	Homo sapiens	Q9Y5P3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X), FASTA

>8ARI_1 C-terminal-binding protein 1 (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X)
HHHHHHSAGLEVLFQGPMGSSHLLNKGLPLGVRPPIMNGPLHPRPLVALLDGRDCTVEMP
ILKDVATVAFCDAQSTQEIHEKVLNEAVGALMYHTITLTREDLEKFKALRIIVRIGSGFD
NIDIKSAGDLGIAVCNVPAASVEETADSTLCHILNLYRRATWLHQALREGTRVQSVEQIR
EVASGAARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSDGVERALGLQRVSTL
QDLLFHSDCVTLHCGLNEHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKEGR
IRGAALDVHESEPFSFSQGPLKDAPNLICTPHAAWYSEQASIEMREEAAREIRRAITGRI
PDSLKNCVNKDHLTAATHWASMDPAVVHPELNGAAYRYPPGVVGVAPTGIPAAVEGIVPS
AMSLSHGLPPVAHPPHAPSPGQTVKPEADRDHASDQL

Sequence of entity 2 (a, b, c, d, e, f, g, h, i, j), FASTA

>8ARI_2 Retinoic acid-induced protein 2 (chains a, b, c, d, e, f, g, h, i, j)
HHHHHHPMKQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTF
TVTEGSGSGSENLYFQGAMDSRHTVIKMGSENEALDLSMKSVPWLKAGALDLSVAAHRKS
EPPPETLYD

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	24

Primary citation

Cryo-EM structure of human CtBP1/RAI2(303-362) delta(331-341) filament. Goradia, N., Mullapudi, E., Wilmanns, M. To be published.

Other PDB entries of the same protein (UniProt Q13363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MX3 1.95 Å, Crystal structure of CtBP dehydrogenase core holo form
4U6S 2.1 Å, CtBP1 in complex with substrate phenylpyruvate
9WRJ 2.2 Å, Crystal structure of CtBP1 in complex with PALI1
4U6Q 2.3 Å, CtBP1 bound to inhibitor 2-(hydroxyimino)-3-phenylpropanoic acid
7KWM 2.3 Å, CtBP1 (28-375) L182F/V185T - AMP
6V8A 2.35 Å, Human CtBP1 (28-375) in complex with AMP
4LCE 2.38 Å, CtBP1 in complex with substrate MTOB
6CDR 2.4 Å, Human CtBP1 (28-378)
6V89 2.45 Å, Human CtBP1 (28-375) in complex with AMP
6CDF 2.6 Å, Human CtBP1 (28-378)

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