1XO5 | pdb_00001xo5

Crystal structure of CIB1, an EF-hand, integrin and kinase-binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.257 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1XO5

This is version 1.4 of the entry. See complete history

Literature

Structural and Biochemical Characterization of CIB1 Delineates a New Family of EF-hand-containing Proteins

Gentry, H.R.Singer, A.U.Betts, L.Yang, C.Ferrara, J.D.Sondek, J.Parise, L.V.

(2005) J Biological Chem 280: 8407-8415

  • DOI: https://doi.org/10.1074/jbc.M411515200
  • Primary Citation Related Structures: 
    1XO5

  • PubMed Abstract: 

    CIB1 (CIB) is an EF-hand-containing protein that binds multiple effector proteins, including the platelet alphaIIbbeta3 integrin and several serine/threonine kinases and potentially modulates their function. The crystal structure for Ca(2+)-bound CIB1 has been determined at 2.0 A resolution and reveals a compact alpha-helical protein containing four EF-hands, the last two of which bind calcium ions in the standard fashion seen in many other EF-hand proteins. CIB1 shares high structural similarity with calcineurin B and the neuronal calcium sensor (NCS) family of EF-hand-containing proteins. Most importantly, like calcineurin B and NCS proteins, which possess a large hydrophobic pocket necessary for ligand binding, CIB1 contains a hydrophobic pocket that has been implicated in ligand binding by previous mutational analysis. However, unlike several NCS proteins, Ca(2+)-bound CIB1 is largely monomeric whether bound to a relevant peptide ligand or ligand-free. Differences in structure, oligomeric state, and phylogeny define a new family of CIB1-related proteins that extends from arthropods to humans.


  • Organizational Affiliation
    • Department of Pharmacology, The University of North Carolina, Chapel Hill 27599-7365, USA.

Macromolecule Content 

  • Total Structure Weight: 42.28 kDa 
  • Atom Count: 3,186 
  • Modeled Residue Count: 344 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calcium and integrin-binding protein 1
A, B
183Homo sapiensMutation(s): 0 
Gene Names: CIB1PRKDCIPKIPCIB
UniProt & NIH Common Fund Data Resources
Find proteins for Q99828 (Homo sapiens)
Explore Q99828 
Go to UniProtKB:  Q99828
PHAROS:  Q99828
GTEx:  ENSG00000185043 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99828
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.663α = 90
b = 51.009β = 103.12
c = 77.214γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations