Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 31.17 kDa 
• Atom Count: 2321 
• Modelled Residue Count: 278 
• Deposited Residue Count: 281 
• Unique protein chains: 2

5E0Q

Crystal structure of the Nup98 C-terminal domain bound to nanobody TP377

• PDB DOI: 10.2210/pdb5E0Q/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Vicugna pacos, Xenopus tropicalis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-09-29 Released: 2015-12-16 
• Deposition Author(s): Pleiner, T., Trakhanov, S., Goerlich, D.
• Funding Organization(s): Deutsche

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7NOW 7NQA

Literature

Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation.

Pleiner, T., Bates, M., Trakhanov, S., Lee, C.T., Schliep, J.E., Chug, H., Bohning, M., Stark, H., Urlaub, H., Gorlich, D.

(2015) Elife 4: e11349-e11349

• PubMed: 26633879 
• DOI: 10.7554/eLife.11349
• Primary Citation of Related Structures:  
  5E0Q


• PubMed Abstract: 
  

Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target.

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Organizational Affiliation: 

Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-Nup98 Nanobody TP377	A	128	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup98-Nup96	B	153	Xenopus tropicalis	Mutation(s): 1  Gene Names: nup98
UniProt
Find proteins for J7I6Y1 (Xenopus tropicalis) Explore J7I6Y1  Go to UniProtKB:  J7I6Y1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.59	α = 90
b = 66.59	β = 90
c = 87.9	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-09-29 
• Released Date: 2015-12-16 
Deposition Author(s): Pleiner, T., Trakhanov, S., Goerlich, D.

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Funding Organization	Location	Grant Number
Deutsche	Germany	--

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references