3QOR

Crystal structure of human nuclear migration protein NudC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Features and Chaperone Activity of the NudC Protein Family.

Zheng, M.Cierpicki, T.Burdette, A.J.Utepbergenov, D.Janczyk, P.L.Derewenda, U.Stukenberg, P.T.Caldwell, K.A.Derewenda, Z.S.

(2011) J Mol Biol 409: 722-741

  • DOI: https://doi.org/10.1016/j.jmb.2011.04.018
  • Primary Citation of Related Structures:  
    3QOR

  • PubMed Abstract: 

    The NudC family consists of four conserved proteins with representatives in all eukaryotes. The archetypal nudC gene from Aspergillus nidulans is a member of the nud gene family that is involved in the maintenance of nuclear migration. This family also includes nudF, whose human orthologue, Lis1, codes for a protein essential for brain cortex development. Three paralogues of NudC are known in vertebrates: NudC, NudC-like (NudCL), and NudC-like 2 (NudCL2). The fourth distantly related member of the family, CML66, contains a NudC-like domain. The three principal NudC proteins have no catalytic activity but appear to play as yet poorly defined roles in proliferating and dividing cells. We present crystallographic and NMR studies of the human NudC protein and discuss the results in the context of structures recently deposited by structural genomics centers (i.e., NudCL and mouse NudCL2). All proteins share the same core CS domain characteristic of proteins acting either as cochaperones of Hsp90 or as independent small heat shock proteins. However, while NudC and NudCL dimerize via an N-terminally located coiled coil, the smaller NudCL2 lacks this motif and instead dimerizes as a result of unique domain swapping. We show that NudC and NudCL, but not NudCL2, inhibit the aggregation of several target proteins, consistent with an Hsp90-independent heat shock protein function. Importantly, and in contrast to several previous reports, none of the three proteins is able to form binary complexes with Lis1. The availability of structural information will be of help in further studies on the cellular functions of the NudC family.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear migration protein nudC121Homo sapiensMutation(s): 2 
Gene Names: NUDC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y266 (Homo sapiens)
Explore Q9Y266 
Go to UniProtKB:  Q9Y266
GTEx:  ENSG00000090273 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y266
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear migration protein nudC121Homo sapiensMutation(s): 2 
Gene Names: NUDC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y266 (Homo sapiens)
Explore Q9Y266 
Go to UniProtKB:  Q9Y266
GTEx:  ENSG00000090273 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y266
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear migration protein nudC121Homo sapiensMutation(s): 2 
Gene Names: NUDC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y266 (Homo sapiens)
Explore Q9Y266 
Go to UniProtKB:  Q9Y266
GTEx:  ENSG00000090273 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y266
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear migration protein nudC
D, E
121Homo sapiensMutation(s): 2 
Gene Names: NUDC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y266 (Homo sapiens)
Explore Q9Y266 
Go to UniProtKB:  Q9Y266
GTEx:  ENSG00000090273 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y266
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
OCS
Query on OCS
D, E
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.734α = 90
b = 51.82β = 90.58
c = 92.854γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
SHELXEmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance