7NXX | pdb_00007nxx

Structure of Superoxide Dismutase 1 (SOD1) in complex with nanobody 2 (Nb2).

• PDB DOI: https://doi.org/10.2210/pdb7NXX/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens, Camelus dromedarius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-03-19 Released: 2022-09-28 
• Deposition Author(s): Gallardo, R., Rousseau, F., Schymkowitz, J., Ulens, C.
• Funding Organization(s): Research Foundation - Flanders (FWO), KU Leuven

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.245 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Identification and rational improvement of a nanobody that suppresses aggregation of mutant SOD1

van der Kant, R., Gallardo, R., Michiels, E., Wilkinson, H., Claes, F., Laird, A., Van Den Bosch, L., Robberecht, W., Ghassabeh, G.H., Oliveberg, M., Ulens, C., Schymkowitz, J., Rousseau, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.71 kDa 
• Atom Count: 2,145 
• Modeled Residue Count: 289 
• Deposited Residue Count: 289 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A	153	Homo sapiens	Mutation(s): 0  Gene Names: SOD1 EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
PHAROS:  P00441 GTEx:  ENSG00000142168

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody 2	B	136	Camelus dromedarius	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.245 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.83	α = 90
b = 115.83	β = 90
c = 83.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Gallardo, R., Rousseau, F., Schymkowitz, J., Ulens, C.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0C1319N
KU Leuven	Belgium	C14/17/093
Research Foundation - Flanders (FWO)	Belgium	G0H1716N
KU Leuven	Belgium	C24/17/075

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary