2MUZ | pdb_00002muz

ssNMR structure of a designed rocker protein

• PDB DOI: https://doi.org/10.2210/pdb2MUZ/pdb
• BMRB: 25236

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2014-09-18 Released: 2014-12-24 
• Deposition Author(s): Wang, T., Joh, N., Wu, Y., DeGrado, W.F., Hong, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 
• Selection Criteria: structures with the least restraint violations 

Literature

De novo design of a transmembrane Zn2+-transporting four-helix bundle.

Joh, N.H., Wang, T., Bhate, M.P., Acharya, R., Wu, Y., Grabe, M., Hong, M., Grigoryan, G., DeGrado, W.F.

(2014) Science 346: 1520-1524

• PubMed: 25525248 
• DOI: https://doi.org/10.1126/science.1261172
• Primary Citation Related Structures: 
  2MUZ, 4P6J, 4P6K, 4P6L


• PubMed Abstract: 
  

  The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn(2+) and Co(2+), but not Ca(2+), across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn(2+) ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India.
Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. [e-mail] [e-mail] [e-mail] [e-mail].
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. [e-mail] [e-mail] [e-mail] [e-mail].
Department of Computer Science and Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA. [e-mail] [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.89 kDa 
• Atom Count: 464 
• Modeled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed rocker protein	A, B, C, D	26	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PFF	A, B, C, D	L-PEPTIDE LINKING	C9 H10 F N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Wang, T., Joh, N., Wu, Y., DeGrado, W.F., Hong, M.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary