4ZDR

Crystal structure of 14-3-3[zeta]-LKB1 fusion protein

• PDB DOI: https://doi.org/10.2210/pdb4ZDR/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-04-18 Released: 2015-09-09 
• Deposition Author(s): Ding, S., Shi, Z.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.191 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Structure of the 14-3-3 zeta-LKB1 fusion protein provides insight into a novel ligand-binding mode of 14-3-3.

Ding, S., Zhou, R., Zhu, Y.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1114-1119

• PubMed: 26323294 
• DOI: https://doi.org/10.1107/S2053230X15012595
• Primary Citation of Related Structures:  
  4ZDR


• PubMed Abstract: 
  

  The 14-3-3 proteins are a family of highly conserved proteins that play key roles in many cellular processes. The tumour suppressor LKB1 regulates cell polarity, cell growth and energy metabolism. 14-3-3 proteins bind to LKB1 and suppress its functions. Previously, preliminary crystallographic data for the 14-3-3ζ-LKB1 fusion protein have been reported. Here, the crystal structure of this fusion protein was solved and a novel potential binding mode of 14-3-3 to its ligands was found.

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Organizational Affiliation: 

Department of General Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai 200011, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.43 kDa 
• Atom Count: 3,754 
• Modelled Residue Count: 484 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta,GGSGGS linker,Serine/threonine-protein kinase STK11	A, B	266	Homo sapiens, synthetic construct	Mutation(s): 1  Gene Names: YWHAZ, STK11, LKB1, PJS EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15831 (Homo sapiens) Explore Q15831  Go to UniProtKB:  Q15831
PHAROS:  Q15831 GTEx:  ENSG00000118046
Find proteins for P63104 (Homo sapiens) Explore P63104  Go to UniProtKB:  P63104
PHAROS:  P63104 GTEx:  ENSG00000164924
UniProt Groups	Q15831P63104

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
TME	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	PROPANE C3 H8 ATUOYWHBWRKTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.191 
• R-Value Observed: 0.196 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.262	α = 90
b = 130.262	β = 90
c = 264.96	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Ding, S., Shi, Z.B.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description