7QF7 | pdb_00007qf7

Orthorhombic crystal structure of PTG CBM21 in complex with beta-cyclodextrin

• PDB DOI: https://doi.org/10.2210/pdb7QF7/pdb

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


• Deposited: 2021-12-04 Released: 2022-11-02 
• Deposition Author(s): Semrau, M.S., Storici, P., Lolli, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.195 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Molecular architecture of the glycogen- committed PP1/PTG holoenzyme.

Semrau, M.S., Giachin, G., Covaceuszach, S., Cassetta, A., Demitri, N., Storici, P., Lolli, G.

(2022) Nat Commun 13: 6199-6199

• PubMed: 36261419 
• DOI: https://doi.org/10.1038/s41467-022-33693-z
• Primary Citation Related Structures: 
  7QF7, 7QFA, 7QFB, 7QM2


• PubMed Abstract: 
  

  The delicate alternation between glycogen synthesis and degradation is governed by the interplay between key regulatory enzymes altering the activity of glycogen synthase and phosphorylase. Among these, the PP1 phosphatase promotes glycogenesis while inhibiting glycogenolysis. PP1 is, however, a master regulator of a variety of cellular processes, being conveniently directed to each of them by scaffolding subunits. PTG, Protein Targeting to Glycogen, addresses PP1 action to glycogen granules. In Lafora disease, the most aggressive pediatric epilepsy, genetic alterations leading to PTG accumulation cause the deposition of insoluble polyglucosans in neurons. Here, we report the crystallographic structure of the ternary complex PP1/PTG/carbohydrate. We further refine the mechanism of the PTG-mediated PP1 recruitment to glycogen by identifying i) an unusual combination of recruitment sites, ii) their contributions to the overall binding affinity, and iii) the conformational heterogeneity of this complex by in solution SAXS analyses.

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Organizational Affiliation: 
• Department of Cellular, Computational and Integrative Biology - CIBio, University of Trento, via Sommarive 9, 38123, Povo, Trento, Italy.
Protein Facility, Elettra Sincrotrone Trieste S.C.p.A, SS 14 - km 163,5 in AREA Science Park, 34149, Basovizza, Trieste, Italy.
Department of Chemical Sciences (DiSC), University of Padua, via F. Marzolo 1, 35131, Padova, Italy.
Institute of Crystallography - C.N.R.- Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149, Trieste, Italy.
XRD2 Beamline, Elettra Sincrotrone Trieste S.C.p.A, SS 14 - km 163,5 in AREA Science Park, 34149, Basovizza, Trieste, Italy.
Protein Facility, Elettra Sincrotrone Trieste S.C.p.A, SS 14 - km 163,5 in AREA Science Park, 34149, Basovizza, Trieste, Italy. [e-mail].
Department of Cellular, Computational and Integrative Biology - CIBio, University of Trento, via Sommarive 9, 38123, Povo, Trento, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.82 kDa 
• Atom Count: 1,276 
• Modeled Residue Count: 129 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase 1 regulatory subunit 3C	A	134	Homo sapiens	Mutation(s): 0  Gene Names: PPP1R3C, PPP1R5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQK1 (Homo sapiens) Explore Q9UQK1  Go to UniProtKB:  Q9UQK1
PHAROS:  Q9UQK1 GTEx:  ENSG00000119938

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	B [auth C]	7		N/A
Glycosylation Resources
GlyTouCan: G01435GL GlyCosmos: G01435GL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012	B [auth C]	beta-cyclodextrin	Oligosaccharide / Drug delivery

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.195 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.593	α = 90
b = 56.443	β = 90
c = 70.553	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Semrau, M.S., Storici, P., Lolli, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description