6W90 | pdb_00006w90

De novo designed NTF2 fold protein NT-9

• PDB DOI: https://doi.org/10.2210/pdb6W90/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-21 Released: 2020-08-19 
• Deposition Author(s): Thompson, M.C., Pan, X., Liu, L., Fraser, J.S., Kortemme, T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.210 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: in silico

Literature

Expanding the space of protein geometries by computational design of de novo fold families.

Pan, X., Thompson, M.C., Zhang, Y., Liu, L., Fraser, J.S., Kelly, M.J.S., Kortemme, T.

(2020) Science 369: 1132-1136

• PubMed: 32855341 
• DOI: https://doi.org/10.1126/science.abc0881
• Primary Citation Related Structures: 
  6VG7, 6VGA, 6VGB, 6W90


• PubMed Abstract: 
  

  Naturally occurring proteins vary the precise geometries of structural elements to create distinct shapes optimal for function. We present a computational design method, loop-helix-loop unit combinatorial sampling (LUCS), that mimics nature's ability to create families of proteins with the same overall fold but precisely tunable geometries. Through near-exhaustive sampling of loop-helix-loop elements, LUCS generates highly diverse geometries encompassing those found in nature but also surpassing known structure space. Biophysical characterization showed that 17 (38%) of 45 tested LUCS designs encompassing two different structural topologies were well folded, including 16 with designed non-native geometries. Four experimentally solved structures closely matched the designs. LUCS greatly expands the designable structure space and offers a new paradigm for designing proteins with tunable geometries that may be customizable for novel functions.

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Organizational Affiliation: 
• Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. [e-mail] [e-mail].
UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA.
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Chan Zuckerberg Biohub, San Francisco, CA, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.53 kDa 
• Atom Count: 1,344 
• Modeled Residue Count: 130 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTF2 fold protein loop-helix-loop design NT-9	A	131	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PE	B [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C41 H82 N O8 P LVNGJLRDBYCPGB-LDLOPFEMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.210 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.5	α = 90
b = 51.99	β = 90
c = 66.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Thompson, M.C., Pan, X., Liu, L., Fraser, J.S., Kortemme, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM110089

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2020-09-09
  Changes: Database references
• Version 2.0: 2024-03-06
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-04-03
  Changes: Refinement description