8ATI | pdb_00008ati

Human CtBP2(31-364) in complex with RAI2 peptide(315-322)

• PDB DOI: https://doi.org/10.2210/pdb8ATI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-23 Released: 2023-08-23 
• Deposition Author(s): Mullapudi, E., Goradia, N., Wilmanns, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.228 (DCC) 

Starting Model: experimental

Literature

Human CtBP2(31-364) in complex with RAI2 peptide(315-322)

Goradia, N., Mullapudi, E., Wilmanns, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 237.6 kDa 
• Atom Count: 10,746 
• Modeled Residue Count: 1,331 
• Deposited Residue Count: 2,141 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of C-terminal-binding protein 2	A, B, C, D	353	Homo sapiens	Mutation(s): 0  Gene Names: CTBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P56545 (Homo sapiens) Explore P56545  Go to UniProtKB:  P56545
PHAROS:  P56545 GTEx:  ENSG00000175029

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid-induced protein 2	E [auth a], F [auth b], G [auth c]	243	Homo sapiens	Mutation(s): 0  Gene Names: RAI2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5P3 (Homo sapiens) Explore Q9Y5P3  Go to UniProtKB:  Q9Y5P3
PHAROS:  Q9Y5P3 GTEx:  ENSG00000131831

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	H [auth A], I [auth B], J [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PEG (Subject of Investigation/LOI)	L [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.228 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.646	α = 90
b = 126.646	β = 90
c = 357.598	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Mullapudi, E., Goradia, N., Wilmanns, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	218826742

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary