7NQ6 | pdb_00007nq6

High resolution crystal structure of C-terminal domain (residues 715-866) of Nucleoporin-98

• PDB DOI: https://doi.org/10.2210/pdb7NQ6/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Xenopus tropicalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-03-01 Released: 2021-04-07 
• Deposition Author(s): Trakhanov, S., Goerlich, D., Huyton, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.192 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

High resolution crystal structure of C-terminal domain (residues 715-866) of Nucleoporin-98

Trakhanov, S., Huyton, T., Goerlich, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.57 kDa 
• Atom Count: 1,464 
• Modeled Residue Count: 152 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup96	A	152	Xenopus tropicalis	Mutation(s): 0  Gene Names: nup98
UniProt
Find proteins for J7I6Y1 (Xenopus tropicalis) Explore J7I6Y1  Go to UniProtKB:  J7I6Y1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD (Subject of Investigation/LOI)	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.192 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.07	α = 90
b = 72.07	β = 90
c = 91.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Trakhanov, S., Goerlich, D., Huyton, T.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description