7NOW

Complex of Nucleoporin-98 and nanobody MS98-27 solved at 1.85A resolution

• PDB DOI: https://doi.org/10.2210/pdb7NOW/pdb

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


• Deposited: 2021-02-26 Released: 2021-04-07 
• Deposition Author(s): Sola-Colom, M., Trakhanov, S., Goerlich, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.209 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5E0Q

Literature

Complex of Nucleoporin-98 and nanobody MS98-27 solved at 1.85A resolution

Sola-Colom, M., Trakhanov, S., Goerlich, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.84 kDa 
• Atom Count: 4,822 
• Modelled Residue Count: 563 
• Deposited Residue Count: 564 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-Nup98 nanobody MS98-27	A, C	129	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup98	B, D	153	Xenopus tropicalis	Mutation(s): 0  Gene Names: nup98
UniProt
Find proteins for A0A6I8SCP2 (Xenopus tropicalis) Explore A0A6I8SCP2  Go to UniProtKB:  A0A6I8SCP2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	F [auth B], G [auth C], I [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA (Subject of Investigation/LOI)	E [auth B], H [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.209 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.7554/ELIFE.11349

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.8	α = 90
b = 149.81	β = 133.089
c = 85.09	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): Sola-Colom, M., Trakhanov, S., Goerlich, D.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2023-08-02
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description