6MDR | pdb_00006mdr

Cryo-EM structure of the Ceru+32/GFP-17 protomer

• PDB DOI: https://doi.org/10.2210/pdb6MDR/pdb
• EM Map EMD-9104: EMDB EMDataResource

• Classification: LUMINESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-09-05 Released: 2019-01-23 
• Deposition Author(s): Simon, A.J., Zhou, Y., Ramasubramani, V., Glaser, J., Pothukuchy, A., Golihar, J., Gerberich, J.C., Leggere, J.C., Morrow, B.R., Jung, C., Glotzer, S.C., Taylor, D.W., Ellington, A.D.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Supercharging enables organized assembly of synthetic biomolecules.

Simon, A.J., Zhou, Y., Ramasubramani, V., Glaser, J., Pothukuchy, A., Gollihar, J., Gerberich, J.C., Leggere, J.C., Morrow, B.R., Jung, C., Glotzer, S.C., Taylor, D.W., Ellington, A.D.

(2019) Nat Chem 11: 204-212

• PubMed: 30643229 
• DOI: https://doi.org/10.1038/s41557-018-0196-3
• Primary Citation Related Structures: 
  6MDR


• PubMed Abstract: 
  

  Symmetrical protein oligomers are ubiquitous in biological systems and perform key structural and regulatory functions. However, there are few methods for constructing such oligomers. Here we have engineered completely synthetic, symmetrical oligomers by combining pairs of oppositely supercharged variants of a normally monomeric model protein through a strategy we term 'supercharged protein assembly' (SuPrA). We show that supercharged variants of green fluorescent protein can assemble into a variety of architectures including a well-defined symmetrical 16-mer structure that we solved using cryo-electron microscopy at 3.47 Å resolution. The 16-mer is composed of two stacked rings of octamers, in which the octamers contain supercharged proteins of alternating charges, and interactions within and between the rings are mediated by a variety of specific electrostatic contacts. The ready assembly of this structure suggests that combining oppositely supercharged pairs of protein variants may provide broad opportunities for generating novel architectures via otherwise unprogrammed interactions.

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Organizational Affiliation: 
• Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
US Army Research Laboratory - South, Austin, TX, USA.
Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.
Department of Materials Science & Engineering, University of Michigan, Ann Arbor, MI, USA.
Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA. [e-mail].
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA. [e-mail].
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. [e-mail].
Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA. [e-mail].
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA. [e-mail].
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 445.21 kDa 
• Atom Count: 29,456 
• Modeled Residue Count: 3,696 
• Deposited Residue Count: 3,896 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ceru+32	A [auth a], C [auth c], E [auth e], G [auth g], I [auth i], K [auth k], M [auth m], O [auth o]	247	Aequorea victoria	Mutation(s): 39  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GFP-17	B [auth b], D [auth d], F [auth f], H [auth h], J [auth j], L [auth l], N [auth n], P [auth p]	240	Aequorea victoria	Mutation(s): 22  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Simon, A.J., Zhou, Y., Ramasubramani, V., Glaser, J., Pothukuchy, A., Golihar, J., Gerberich, J.C., Leggere, J.C., Morrow, B.R., Jung, C., Glotzer, S.C., Taylor, D.W., Ellington, A.D.

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Funding Organization	Location	Grant Number
Other government	United States	W911NF-1-51-0120

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Database references
• Version 1.3: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Refinement description