6QW3 | pdb_00006qw3

Calcium-bound gelsolin domain 2

• PDB DOI: https://doi.org/10.2210/pdb6QW3/pdb

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


• Deposited: 2019-03-05 Released: 2019-08-28 
• Deposition Author(s): Scalone, E., Boni, F., Milani, M., Mastrangelo, E., de Rosa, M.
• Funding Organization(s): Amyloidosis Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

High-resolution crystal structure of gelsolin domain 2 in complex with the physiological calcium ion.

Bollati, M., Scalone, E., Boni, F., Mastrangelo, E., Giorgino, T., Milani, M., de Rosa, M.

(2019) Biochem Biophys Res Commun 518: 94-99

• PubMed: 31416615 
• DOI: https://doi.org/10.1016/j.bbrc.2019.08.013
• Primary Citation Related Structures: 
  6QW3


• PubMed Abstract: 
  

  The second domain of gelsolin (G2) hosts mutations responsible for a hereditary form of amyloidosis. The active form of gelsolin is Ca ²⁺ -bound; it is also a dynamic protein, hence structural biologists often rely on the study of the isolated G2. However, the wild type G2 structure that have been used so far in comparative studies is bound to a crystallographic Cd ²⁺ , in lieu of the physiological calcium. Here, we report the wild type structure of G2 in complex with Ca ²⁺ highlighting subtle ion-dependent differences. Previous findings on different G2 mutations are also briefly revised in light of these results.

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Organizational Affiliation: 
• Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Celoria 26, 20133, Milano, Italy; Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Celoria 26, 20133, Milano, Italy; Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.21 kDa 
• Atom Count: 1,096 
• Modeled Residue Count: 110 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gelsolin	A	119	Homo sapiens	Mutation(s): 0  Gene Names: GSN
UniProt & NIH Common Fund Data Resources
Find proteins for P06396 (Homo sapiens) Explore P06396  Go to UniProtKB:  P06396
PHAROS:  P06396 GTEx:  ENSG00000148180

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.653	α = 90
b = 50.275	β = 90
c = 70.819	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Scalone, E., Boni, F., Milani, M., Mastrangelo, E., de Rosa, M.

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Funding Organization	Location	Grant Number
Amyloidosis Foundation	United States	--

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary