8ATI: Human CtBP2(31-364)

Human CtBP2(31-364) in complex with RAI2 peptide(315-322). Determined by X-ray diffraction at 2.6 Å resolution. Released 23 Aug 2023.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 7
Atoms: 10,746
Mol. weight: 237.6 kDa
Ligands: NAD
Released: 23 Aug 2023

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

Secondary structure: helices and β-sheets

8ATI contains 77 α-helices and 74 β-strands across 7 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 and c: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	317-318	2	1

Chain A: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	35-38	4	1
α-helix	47-51	5
β-strand	56-59	4	1
α-helix	65-67	3
α-helix	70-75	6
β-strand	78-81	4	1
β-strand	87	1	2
α-helix	89-92	4
β-strand	100-103	4	1
β-strand	111	1	2
α-helix	113-118	6
β-strand	122-124	3	1
α-helix	131-147	17
α-helix	149-157	9
α-helix	165-171	7
α-helix	181	1
β-strand	182-186	5	3
α-helix	190-199	10
α-helix	200-202	3
α-helix	204	1
β-strand	205-209	5	3
α-helix	214	1
α-helix	217-221	5
β-strand	224-225	2	3
α-helix	229-235	7
β-strand	238-241	4	3
β-strand	253	1	4
α-helix	255-258	4
α-helix	262	1
β-strand	265-269	5	3
α-helix	273-275	3
β-strand	276	1	4
α-helix	278-286	9
β-strand	290-295	6	3
β-strand	316-318	3	3
α-helix	327-346	20
β-strand	356	1	1

Chain B: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	35-38	4	5
α-helix	47-51	5
β-strand	56-59	4	5
α-helix	65-67	3
α-helix	70-75	6
β-strand	78-81	4	5
β-strand	87	1	6
α-helix	89-92	4
β-strand	100-103	4	5
β-strand	111	1	6
α-helix	113-119	7
β-strand	122-124	3	5
α-helix	131-147	17
α-helix	149-157	9
α-helix	165-171	7
β-strand	182-186	5	7
α-helix	190-199	10
α-helix	200-202	3
β-strand	205-209	5	7
α-helix	214	1
α-helix	217-220	4
β-strand	224-225	2	7
α-helix	229-235	7
β-strand	238-241	4	7
β-strand	253	1	8
α-helix	255-260	6
α-helix	262	1
β-strand	265-269	5	7
α-helix	273-275	3
β-strand	276	1	8
α-helix	278-287	10
β-strand	290-295	6	7
β-strand	316-318	3	7
α-helix	327-346	20
β-strand	356	1	5
α-helix	359-361	3

Chain C: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	35-38	4	9
α-helix	47-51	5
β-strand	56-59	4	9
α-helix	65-67	3
α-helix	70-75	6
β-strand	78-81	4	9
β-strand	87	1	10
α-helix	89-92	4
β-strand	100-103	4	9
β-strand	111	1	10
α-helix	113-118	6
β-strand	122-124	3	9
α-helix	131-147	17
α-helix	149-157	9
α-helix	165-171	7
β-strand	173	1	11
β-strand	175	1	11
α-helix	181	1
β-strand	182-186	5	12
α-helix	190-199	10
α-helix	200-202	3
α-helix	204	1
β-strand	205-209	5	12
α-helix	214	1
α-helix	217-220	4
β-strand	224-225	2	12
α-helix	229-235	7
β-strand	238-241	4	12
β-strand	253	1	13
α-helix	255-258	4
β-strand	265-269	5	12
α-helix	273-275	3
β-strand	276	1	13
α-helix	278-286	9
β-strand	290-295	6	12
β-strand	316-318	3	12
α-helix	327-346	20
β-strand	356	1	9
α-helix	359-361	3

Chain D: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	14
β-strand	36-38	3	15
α-helix	47-51	5
β-strand	56	1	14
α-helix	65-67	3
α-helix	70-75	6
β-strand	78-81	4	15
β-strand	87	1	16
α-helix	89-92	4
β-strand	100-103	4	15
β-strand	111	1	16
α-helix	113-118	6
β-strand	122-124	3	15
α-helix	131-147	17
α-helix	149-157	9
α-helix	165-171	7
α-helix	181	1
β-strand	182-186	5	17
α-helix	190-199	10
α-helix	200-202	3
α-helix	204	1
β-strand	205-209	5	17
β-strand	224-225	2	17
α-helix	229-235	7
β-strand	238-241	4	17
β-strand	253	1	18
α-helix	255-258	4
α-helix	262	1
β-strand	266-269	4	17
α-helix	273-275	3
β-strand	276	1	18
α-helix	278-287	10
β-strand	292-295	4	17
β-strand	316-318	3	17
α-helix	327-346	20
β-strand	356	1	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of C-terminal-binding protein 2	A, B, C, D	protein	353	Homo sapiens	P56545 (AlphaFold model)
Retinoic acid-induced protein 2	a, b, c	protein	243	Homo sapiens	Q9Y5P3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8ATI_1 Isoform 2 of C-terminal-binding protein 2 (chains A, B, C, D)
HHHHHHSAGLEVLFQGPMDHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHEK
VLNEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAV
EETADSTICHILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRT
GQAVAVRAKAFGFSVIFYDPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHH
LINDFTIKQMRQGAFLVNAARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFAQGPLK
DAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGRIPESLRNCVNKEFFVT

Sequence of entity 2 (a, b, c), FASTA

>8ATI_2 Retinoic acid-induced protein 2 (chains a, b, c)
HHHHHHPMKQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTF
TVTEGSGSGSENLYFQGAMDSRHTVIKMGSENEALDLSMKSVPWLKAGEVSPPIFQEDAA
LDAAVAAHRKSEPPPETLYDSGASVDSSGHTVMEKLPSGMEISFAPATSHEAPAMMDSHI
SSSDAATEMLSQPNHPSGEVKAENNIEMVGESQAAKVIVSVEDAVPTIFCGKIKGLSGVS
TKN

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	4

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

Primary citation

Human CtBP2(31-364) in complex with RAI2 peptide(315-322). Goradia, N., Mullapudi, E., Wilmanns, M. To be published.

Other PDB entries of the same protein (UniProt P56545 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WRI 1.85 Å, Crystal structure of CtBP2 in complex with G9a
2OME 2.8 Å, Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)
4LCJ 2.86 Å, CtBP2 in complex with substrate MTOB
6WKW 3.6 Å, EM structure of CtBP2 with a minimal dehydrogenase domain of CtBP2

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