7ZIT | pdb_00007zit

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

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 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.

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Organizational Affiliation: 
• Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic. Electronic address: [e-mail].

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 
• Modeled 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 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

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.

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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