4P6L

Crystal Structure of the Computationally Designed Transmembrane Metallotransporter in Octyl Glucoside

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

  • Deposited: 2014-03-25 Released: 2014-12-24 
  • Deposition Author(s): Joh, N.H., Acharya, R., DeGrado, W.F.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


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

  • DOI: 10.1126/science.1261172
  • Structures With Same Primary Citation

  • 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 ...

    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.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. william.degrado@ucsf.edu gevorg.grigoryan@dartmouth.edu meihong@mit.edu michael.grabe@ucsf.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Computationally Designed Transporter of Zn(II) and proton
A, B
26synthetic constructMutation(s): 0 
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.12α = 90
b = 87.12β = 90
c = 87.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States7U01AI074571
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States3F32GM096727

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2014-12-31
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence