8BZC | pdb_00008bzc

co-soaked stabilizers for ERa - 14-3-3 interaction (884_AZ244)

• PDB DOI: https://doi.org/10.2210/pdb8BZC/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-12-14 Released: 2023-12-27 
• Deposition Author(s): Visser, E.J., Sijbesma, E., Ottmann, C.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Linked-fragment stabilizers of 14-3-3 protein-protein interactions

Visser, E.J., Jaishankar, P., Sijbesma, E., Pennings, M.A.M., Vandenboorn, E.M.F., Renslo, A., Arkin, M.R., Brunsveld, L., Ottmann, C.

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 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.78 kDa 
• Atom Count: 2,290 
• Modeled Residue Count: 241 
• Deposited Residue Count: 241 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	236	Homo sapiens	Mutation(s): 2  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ERalpha peptide	B	5	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SG0 (Subject of Investigation/LOI)	G [auth A]	4-[(~{R})-azanyl(oxidanyl)methyl]-7-propan-2-yloxy-1-benzothiophene-2-carboximidamide C13 H17 N3 O2 S AHQCRVYDVIFTJY-CYBMUJFWSA-N
GEH (Subject of Investigation/LOI)	F [auth A]	2-(4-chloranylphenoxy)-2-methyl-~{N}-(2-sulfanylethyl)propanamide C12 H16 Cl N O2 S NDZCOUBEYALMJI-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.723	α = 90
b = 112.327	β = 90
c = 62.374	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Visser, E.J., Sijbesma, E., Ottmann, C.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	--

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary