9WRI: CtBP2

Crystal structure of CtBP2 in complex with G9a. Determined by X-ray diffraction at 1.85 Å resolution. Released 21 Jan 2026.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,028
Mol. weight: 77.35 kDa
Ligands: NAD
Released: 21 Jan 2026

Explore 9WRI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9WRI contains 41 α-helices and 35 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: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	30-34	5
β-strand	35-38	4	1
α-helix	48-51	4
β-strand	56-59	4	1
α-helix	65-67	3
α-helix	70-75	6
β-strand	76-81	6	1
β-strand	87	1	2
α-helix	89-93	5
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	217-220	4
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	278-287	10
β-strand	290-295	6	3
β-strand	316-318	3	3
α-helix	327-346	20
β-strand	356	1	1

Chain B: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	35-38	4	5
α-helix	48-51	4
β-strand	56-59	4	5
α-helix	65-67	3
α-helix	70-75	6
β-strand	76-81	6	5
β-strand	87	1	6
α-helix	89-93	5
β-strand	100-103	4	5
β-strand	111	1	6
α-helix	113-118	6
β-strand	122-124	3	5
α-helix	131-147	17
α-helix	149-157	9
α-helix	165-171	7
α-helix	181	1
β-strand	182-186	5	7
α-helix	190-199	10
α-helix	200-202	3
α-helix	204	1
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	255-258	4
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

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	888-889	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-terminal-binding protein 2	A, B	protein	336	Homo sapiens	P56545 (AlphaFold model)
Histone-lysine N-methyltransferase EHMT2	C	protein	13	Homo sapiens	Q96KQ7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9WRI_1 C-terminal-binding protein 2 (chains A, B)
SMHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHEKVLNEAVGAMMYHTITLT
REDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTICHILNLYRR
NTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIF
YDPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLV
NAARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQ
ASLEMREAAATEIRRAITGRIPESLRNCVNKEFFVT

Sequence of entity 2 (C), FASTA

>9WRI_2 Histone-lysine N-methyltransferase EHMT2 (chains C)
NKEGDTAWDLTPE

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	2

Primary citation

CtBP1/2 oligomerization promotes G9a-Mediated transcriptional repression. Zhang, B., Jiang, J., Sun, W. et al. J Biol Chem (2025) 302:111063-111063. DOI 10.1016/j.jbc.2025.111063 · PubMed

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

8ATI 2.6 Å, Human CtBP2(31-364) in complex with RAI2 peptide(315-322)
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

Browse structure collections

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