4Z33 | pdb_00004z33

Crystal structure of the syntenin PDZ1 and PDZ2 tandem in complex with the Frizzled 7 C-terminal fragment and PIP2

• PDB DOI: https://doi.org/10.2210/pdb4Z33/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-03-30 Released: 2016-06-29 
• Deposition Author(s): Egea-Jimenez, A.L., Gallardo, R., Garcia-Pino, A., Ivarsson, Y., Wawrzyniak, A.M., Kashyap, R., Loris, R., Schymkowitz, J., Rousseau, F., Zimmermann, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the syntenin PDZ1 and PDZ2 tandem in complex with the Frizzled 7 C-terminal fragment and PIP2

Egea-Jimenez, A.L., Gallardo, R., Garcia-Pino, A., Ivarsson, Y., Wawrzyniak, A.M., Kashyap, R., Loris, R., Schymkowitz, J., Rousseau, F., Zimmermann, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.1 kDa 
• Atom Count: 2,754 
• Modeled Residue Count: 341 
• Deposited Residue Count: 344 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin-1	A, B	166	Homo sapiens	Mutation(s): 0  Gene Names: SDCBP, MDA9, SYCL
UniProt & NIH Common Fund Data Resources
Find proteins for O00560 (Homo sapiens) Explore O00560  Go to UniProtKB:  O00560
PHAROS:  O00560 GTEx:  ENSG00000137575

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-GLY-GLU-THR-ALA-VAL	C, D	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75084 (Homo sapiens) Explore O75084  Go to UniProtKB:  O75084
PHAROS:  O75084 GTEx:  ENSG00000155760

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IP2	H [auth A]	D-MYO-INOSITOL-4,5-BISPHOSPHATE C6 H14 O12 P2 MCKAJXMRULSUKI-UZAAGFTCSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], I [auth B], J [auth B], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.744	α = 90
b = 71.744	β = 90
c = 126.36	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Egea-Jimenez, A.L., Gallardo, R., Garcia-Pino, A., Ivarsson, Y., Wawrzyniak, A.M., Kashyap, R., Loris, R., Schymkowitz, J., Rousseau, F., Zimmermann, P.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description