7NQA

Crystal structure of Nucleoporin-98 nanobody MS98-6 complex solved at 2.2A resolution

• PDB DOI: https://doi.org/10.2210/pdb7NQA/pdb

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


• Deposited: 2021-03-01 Released: 2021-07-21 
• Deposition Author(s): Sola-Colom, M., Trakhanov, S., Goerlich, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Crystal structure of Nucleoporin-98 nanobody MS98-6 complex solved at 2.2A 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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.68 kDa 
• Atom Count: 4,657 
• Modelled Residue Count: 552 
• Deposited Residue Count: 552 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup98-Nup96	A, C [auth B]	152	Xenopus tropicalis	Mutation(s): 0  Gene Names: nup98
UniProt
Find proteins for A0A6I8SCP2 (Xenopus tropicalis) Explore A0A6I8SCP2  Go to UniProtKB:  A0A6I8SCP2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-Nup98 Nanobody MS98-6	B [auth D], D [auth C]	124	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS (Subject of Investigation/LOI)	E [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NA (Subject of Investigation/LOI)	F [auth D], G [auth C], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.226 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.76	α = 90
b = 96.63	β = 90
c = 100.87	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: 2021-07-21 
Deposition Author(s): Sola-Colom, M., Trakhanov, S., Goerlich, D.

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2022-09-28
  Changes: Database references, Structure summary
• Version 1.2: 2023-08-02
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.4: 2024-04-03
  Changes: Database references, Structure summary