Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.63 kDa 
• Atom Count: 2480 
• Modelled Residue Count: 312 
• Deposited Residue Count: 502 
• Unique protein chains: 2

1KO6

Crystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98

• DOI: 10.2210/pdb1KO6/pdb

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


• Deposited: 2001-12-20 Released: 2002-09-04 
• Deposition Author(s): Hodel, A.E., Hodel, M.R., Griffis, E.R., Hennig, K.A., Ratner, G.A., Songli, X., Powers, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.247 

Literature

The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98.

Hodel, A.E., Hodel, M.R., Griffis, E.R., Hennig, K.A., Ratner, G.A., Xu, S., Powers, M.A.

(2002) Mol Cell 10: 347-358

• PubMed: 12191480 
• DOI: 10.1016/s1097-2765(02)00589-0
• Primary Citation of Related Structures:  
  1KO6


• PubMed Abstract: 
  

Nup98 is a component of the nuclear pore that plays its primary role in the export of RNAs. Nup98 is expressed in two forms, derived from alternate mRNA splicing. Both forms are processed into two peptides through autoproteolysis mediated by the C-terminal domain of hNup98. The three-dimensional structure of the C-terminal domain reveals a novel protein fold, and thus a new class of autocatalytic proteases. The structure further reveals that the suggested nucleoporin RNA binding motif is unlikely to bind to RNA. The C terminus also contains sequences that target hNup98 to the nuclear pore complex. Noncovalent interactions between the C-terminal domain and the cleaved peptide tail are visible and suggest a model for cleavage-dependent targeting of hNup98 to the nuclear pore.

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Organizational Affiliation: 

Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear Pore Complex Protein Nup98	A, C	187	Homo sapiens	Mutation(s): 0  Gene Names: NUP98, ADAR2 EC: 3.4.21
Find proteins for P52948 (Homo sapiens) Explore P52948  Go to UniProtKB:  P52948
NIH Common Fund Data Resources
PHAROS:  P52948 GTEx:  ENSG00000110713

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear Pore Complex Protein Nup98	B, D	64	Homo sapiens	Mutation(s): 0  Gene Names: NUP98, ADAR2 EC: 3.4.21
Find proteins for P52948 (Homo sapiens) Explore P52948  Go to UniProtKB:  P52948
NIH Common Fund Data Resources
PHAROS:  P52948 GTEx:  ENSG00000110713

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.247 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.9	α = 90
b = 89.9	β = 90
c = 203.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-20 
• Released Date: 2002-09-04 
Deposition Author(s): Hodel, A.E., Hodel, M.R., Griffis, E.R., Hennig, K.A., Ratner, G.A., Songli, X., Powers, M.A.

Revision History  

• Version 1.0: 2002-09-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance