6FIE

Crystallographic structure of calcium loaded Calbindin-D28K.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The X-ray structure of human calbindin-D28K: an improved model.

Noble, J.W.Almalki, R.Roe, S.M.Wagner, A.Duman, R.Atack, J.R.

(2018) Acta Crystallogr D Struct Biol 74: 1008-1014

  • DOI: 10.1107/S2059798318011610

  • PubMed Abstract: 
  • Calbindin-D28K is a widely expressed calcium-buffering cytoplasmic protein that is involved in many physiological processes. It has been shown to interact with other proteins, suggesting a role as a calcium sensor. Many of the targets of calbindin-D2 ...

    Calbindin-D28K is a widely expressed calcium-buffering cytoplasmic protein that is involved in many physiological processes. It has been shown to interact with other proteins, suggesting a role as a calcium sensor. Many of the targets of calbindin-D28K are of therapeutic interest: for example, inositol monophosphatase, the putative target of lithium therapy in bipolar disorder. Presented here is the first crystal structure of human calbindin-D28K. There are significant deviations in the tertiary structure when compared with the NMR structure of rat calbindin-D28K (PDB entry 2g9b), despite 98% sequence identity. Small-angle X-ray scattering (SAXS) indicates that the crystal structure better predicts the properties of calbindin-D28K in solution compared with the NMR structure. Here, the first direct visualization of the calcium-binding properties of calbindin-D28K is presented. Four of the six EF-hands that make up the secondary structure of the protein contain a calcium-binding site. Two distinct conformations of the N-terminal EF-hand calcium-binding site were identified using long-wavelength calcium single-wavelength anomalous dispersion (SAD). This flexible region has previously been recognized as a protein-protein interaction interface. SAXS data collected in both the presence and absence of calcium indicate that there are no large structural differences in the globular structure of calbindin-D28K between the calcium-loaded and unloaded proteins.


    Organizational Affiliation

    School Of Life Sciences, University Of Sussex, Falmer, Brighton BN1 9QG, England.,Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, Wales.,Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, England.,Sussex Drug Discovery Centre, University Of Sussex, Falmer, Brighton BN1 9QG, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calbindin
B
264Homo sapiensMutation(s): 0 
Gene Names: CALB1 (CAB27)
Find proteins for P05937 (Homo sapiens)
Go to Gene View: CALB1
Go to UniProtKB:  P05937
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
B
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 84.617α = 90.00
b = 104.222β = 90.00
c = 29.614γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
AutoPROCdata scaling
BUCCANEERmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references