8W68 | pdb_00008w68

Crystal structure of Q9PR55 at pH 6.0 (use NMR model)

• PDB DOI: https://doi.org/10.2210/pdb8W68/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Ureaplasma parvum serovar 3 str. ATCC 700970
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-28 Released: 2024-02-07 
• Deposition Author(s): Hsu, M.F., Ko, T.P., Huang, K.F., Chen, Y.R., Huang, J.S., Hsu, S.T.D.
• Funding Organization(s): Academia Sinica (Taiwan), National Science Council (NSC, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.260 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: other

Literature

Structure, dynamics, and stability of the smallest and most complex 7 1 protein knot.

Hsu, M.F., Sriramoju, M.K., Lai, C.H., Chen, Y.R., Huang, J.S., Ko, T.P., Huang, K.F., Hsu, S.D.

(2023) J Biological Chem 300: 105553-105553

• PubMed: 38072060 
• DOI: https://doi.org/10.1016/j.jbc.2023.105553
• Primary Citation Related Structures: 
  8IWA, 8IWB, 8IWC, 8W68


• PubMed Abstract: 
  

  Proteins can spontaneously tie a variety of intricate topological knots through twisting and threading of the polypeptide chains. Recently developed artificial intelligence algorithms have predicted several new classes of topological knotted proteins, but the predictions remain to be authenticated experimentally. Here, we showed by X-ray crystallography and solution-state NMR spectroscopy that Q9PR55, an 89-residue protein from Ureaplasma urealyticum, possesses a novel 7 ₁ knotted topology that is accurately predicted by AlphaFold 2, except for the flexible N terminus. Q9PR55 is monomeric in solution, making it the smallest and most complex knotted protein known to date. In addition to its exceptional chemical stability against urea-induced unfolding, Q9PR55 is remarkably robust to resist the mechanical unfolding-coupled proteolysis by a bacterial proteasome, ClpXP. Our results suggest that the mechanical resistance against pulling-induced unfolding is determined by the complexity of the knotted topology rather than the size of the molecule.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Higashihiroshima, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.97 kDa 
• Atom Count: 5,301 
• Modeled Residue Count: 627 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein UU089.1	A, B, C, D, E, F, G, H	89	Ureaplasma parvum serovar 3 str. ATCC 700970	Mutation(s): 0  Gene Names: UU089.1
UniProt
Find proteins for Q9PR55 (Ureaplasma parvum serovar 3 (strain ATCC 700970)) Explore Q9PR55  Go to UniProtKB:  Q9PR55

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.260 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.433	α = 90
b = 54.144	β = 92.07
c = 77.184	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Hsu, M.F., Ko, T.P., Huang, K.F., Chen, Y.R., Huang, J.S., Hsu, S.T.D.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-IDR-112-04
Academia Sinica (Taiwan)	Taiwan	AS-CDA-109-L08
National Science Council (NSC, Taiwan)	Taiwan	110-2113-M-001-050-MY3
National Science Council (NSC, Taiwan)	Taiwan	110-2311-B-001-013-MY3

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release