1G8I | pdb_00001g8i

CRYSTAL STRUCTURE OF HUMAN FREQUENIN (NEURONAL CALCIUM SENSOR 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.263 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1G8I

This is version 1.3 of the entry. See complete history

Literature

Immunocytochemical localization and crystal structure of human frequenin (neuronal calcium sensor 1).

Bourne, Y.Dannenberg, J.Pollmann, V.Marchot, P.Pongs, O.

(2001) J Biological Chem 276: 11949-11955

  • DOI: https://doi.org/10.1074/jbc.M009373200
  • Primary Citation Related Structures: 
    1G8I

  • PubMed Abstract: 

    Frequenin, a member of a large family of myristoyl-switch calcium-binding proteins, functions as a calcium-ion sensor to modulate synaptic activity and secretion. We show that human frequenin colocalizes with ARF1 GTPase in COS-7 cells and occurs in similar cellular compartments as the phosphatidylinositol-4-OH kinase PI4Kbeta, the mammalian homolog of the yeast kinase PIK1. In addition, the crystal structure of unmyristoylated, calcium-bound human frequenin has been determined and refined to 1.9 A resolution. The overall fold of frequenin resembles those of neurocalcin and the photoreceptor, recoverin, of the same family, with two pairs of calcium-binding EF hands and three bound calcium ions. Despite the similarities, however, frequenin displays significant structural differences. A large conformational shift of the C-terminal region creates a wide hydrophobic crevice at the surface of frequenin. This crevice, which is unique to frequenin and distinct from the myristoyl-binding box of recoverin, may accommodate a yet unknown protein ligand.


  • Organizational Affiliation
    • Architecture et Fonction des Macromolécules Biologiques, CNRS UMR-6098, 13402, Marseille Cedex 20, France. yves@afmb.cnrs-mrs.fr

Macromolecule Content 

  • Total Structure Weight: 45.21 kDa 
  • Atom Count: 3,374 
  • Modeled Residue Count: 368 
  • Deposited Residue Count: 380 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NEURONAL CALCIUM SENSOR 1
A, B
190Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62166 (Homo sapiens)
Explore P62166 
Go to UniProtKB:  P62166
PHAROS:  P62166
GTEx:  ENSG00000107130 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62166
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G



Download:Ideal Coordinates CCD File
I [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
O [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
L [auth B]
M [auth B]
D [auth A],
E [auth A],
F [auth A],
L [auth B],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.263 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.811α = 90
b = 55.524β = 94.25
c = 77.705γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description