6WKW: C-terminal-binding protein 2

EM structure of CtBP2 with a minimal dehydrogenase domain of CtBP2. Determined by electron microscopy at 3.6 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,037
Mol. weight: 149.14 kDa
Ligands: NAD
Released: 2 Dec 2020

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

Secondary structure: helices and β-sheets

6WKW contains 62 α-helices and 70 β-strands across 4 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: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	35-38	4	16
α-helix	48-51	4
β-strand	56-59	4	16
α-helix	65-67	3
α-helix	71-74	4
β-strand	78-81	4	16
β-strand	87	1	17
α-helix	89-92	4
β-strand	100-103	4	16
β-strand	111	1	17
α-helix	113-116	4
β-strand	123-125	3	16
α-helix	131-147	17
α-helix	149-156	8
α-helix	165-171	7
β-strand	184-186	3	18
α-helix	190-198	9
β-strand	207-209	3	18
α-helix	214	1
α-helix	217-220	4
β-strand	224-226	3	18
α-helix	229-233	5
β-strand	238	1	19
β-strand	239-241	3	18
β-strand	253	1	20
α-helix	255-258	4
β-strand	266	1	19
α-helix	273-275	3
β-strand	276	1	20
α-helix	279-287	9
β-strand	293-295	3	21
β-strand	316-318	3	21
α-helix	329-343	15
β-strand	356	1	16

Chain B: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	11
α-helix	48-51	4
α-helix	65-67	3
α-helix	72-75	4
β-strand	78	1	11
β-strand	87	1	12
α-helix	89-92	4
β-strand	100-102	3	13
β-strand	111	1	12
α-helix	113-119	7
β-strand	122-124	3	13
α-helix	131-141	11
α-helix	143-146	4
α-helix	151-157	7
α-helix	165-171	7
β-strand	183-186	4	14
α-helix	191-198	8
β-strand	207-209	3	14
α-helix	214	1
β-strand	224-226	3	14
α-helix	229-233	5
β-strand	238-241	4	14
β-strand	253	1	15
α-helix	258-260	3
β-strand	266-269	4	14
β-strand	276	1	15
α-helix	278-286	9
β-strand	293-295	3	14
β-strand	316-318	3	14
α-helix	329-346	18
β-strand	356	1	13

Chain C: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	6
β-strand	57-59	3	6
α-helix	65-67	3
α-helix	70-74	5
β-strand	78-79	2	6
β-strand	81	1	6
β-strand	87	1	7
β-strand	100-103	4	6
β-strand	111	1	7
α-helix	113-116	4
β-strand	122-125	4	6
α-helix	134-146	13
α-helix	149-157	9
α-helix	165-168	4
β-strand	182-185	4	8
β-strand	186	1	9
α-helix	190-196	7
β-strand	205-208	4	8
α-helix	214	1
β-strand	224-225	2	8
α-helix	229-234	6
β-strand	238-241	4	9
β-strand	253	1	10
α-helix	255-258	4
β-strand	266-269	4	9
α-helix	273-275	3
β-strand	276	1	10
α-helix	279-287	9
β-strand	293-295	3	9
α-helix	303	1
β-strand	316-318	3	9
α-helix	330-346	17

Chain D: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	35-36	2	1
α-helix	47-50	4
β-strand	56-57	2	1
α-helix	65-67	3
α-helix	71-74	4
β-strand	76-78	3	1
β-strand	81	1	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	122-125	4	1
α-helix	134-146	13
α-helix	152-157	6
α-helix	165-171	7
β-strand	182-186	5	3
α-helix	190-199	10
β-strand	205-209	5	3
α-helix	214	1
α-helix	218-221	4
β-strand	224-226	3	3
α-helix	229-232	4
α-helix	233-235	3
β-strand	238-241	4	3
α-helix	243-245	3
β-strand	253	1	4
α-helix	258-260	3
β-strand	266-268	3	3
β-strand	276	1	4
α-helix	278-285	8
β-strand	293-295	3	5
β-strand	316-318	3	5
α-helix	329-344	16
β-strand	356	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-terminal-binding protein 2	A, B, C, D	protein	330	Homo sapiens	P56545 (AlphaFold model)

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

>6WKW_1 C-terminal-binding protein 2 (chains A, B, C, D)
RPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHEKVLNEAVGAMMYHTITLTREDL
EKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTICHILNLYRRNTWL
YQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFYDPY
LQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAAR
GGLVDEKALAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASLE
MREAAATEIRRAITGRIPESLRNCVNKEFF

Ligands and cofactors

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

Primary citation

Cryo-EM structure of CtBP2 confirms tetrameric architecture. Jecrois, A.M., Dcona, M.M., Deng, X. et al. Structure (2021) 29:310. DOI 10.1016/j.str.2020.11.008 · PubMed

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
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

Browse structure collections

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