7ZIT

14-3-3 in complex with SARS-COV2 N phospho-peptide

• PDB DOI: https://doi.org/10.2210/pdb7ZIT/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-04-08 Released: 2022-10-26 
• Deposition Author(s): Eisenreichova, A., Boura, E.
• Funding Organization(s): Czech Academy of Sciences

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.205 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Structural basis for SARS-CoV-2 nucleocapsid (N) protein recognition by 14-3-3 proteins.

Eisenreichova, A., Boura, E.

(2022) J Struct Biol 214: 107879-107879

• PubMed: 35781025 
• DOI: https://doi.org/10.1016/j.jsb.2022.107879
• Primary Citation of Related Structures:  
  7ZIT


• PubMed Abstract: 
  

  14-3-3 proteins are important dimeric scaffolds that regulate the function of hundreds of proteins in a phosphorylation-dependent manner. The SARS-CoV-2 nucleocapsid (N) protein forms a complex with human 14-3-3 proteins upon phosphorylation, which has also been described for other coronaviruses. Here, we report a high-resolution crystal structure of 14-3-3 bound to an N phosphopeptide bearing the phosphoserine 197 in the middle. The structure revealed two copies of the N phosphopeptide bound, each in the central binding groove of each 14-3-3 monomer. A complex network of hydrogen bonds and water bridges between the peptide and 14-3-3 was observed explaining the high affinity of the N protein for 14-3-3 proteins.

---

Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.56 kDa 
• Atom Count: 4,173 
• Modelled Residue Count: 474 
• Deposited Residue Count: 474 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta	A, B	230	Homo sapiens	Mutation(s): 0  Gene Names: YWHAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P63104 (Homo sapiens) Explore P63104  Go to UniProtKB:  P63104
PHAROS:  P63104 GTEx:  ENSG00000164924

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	C, D	7	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	G [auth B]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C, D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.205 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.18	α = 90
b = 83.517	β = 90
c = 111.356	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	refinement
PHENIX	model building
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Eisenreichova, A., Boura, E.

---

Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	61388963

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary