8WF6 | pdb_00008wf6

14-3-3 zeta complexed with S559 phosphorylated peptide derived from GPIb alpha cytoplasmic domain

• PDB DOI: https://doi.org/10.2210/pdb8WF6/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-19 Released: 2024-09-25 
• Deposition Author(s): Shu, Z.M., Zhou, A.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Cryo-EM structure of GPIb-IX Complex

Shu, Z.M., Zhou, A.W.

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 and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.6 kDa 
• Atom Count: 7,160 
• Modeled Residue Count: 922 
• Deposited Residue Count: 1,032 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta	A, B, E [auth C], F [auth D]	246	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
S559 phosphorylated peptide	C [auth Q], D [auth R], G [auth E], H [auth F]	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07359 (Homo sapiens) Explore P07359  Go to UniProtKB:  P07359
PHAROS:  P07359 GTEx:  ENSG00000185245

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	I [auth C], J [auth D]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C [auth Q], D [auth R], G [auth E], H [auth F]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.31	α = 90
b = 112.24	β = 97.52
c = 83.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Shu, Z.M., Zhou, A.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Derived calculations, Structure summary