4P6K

Crystal Structure of the Computationally Designed Transmembrane Metallotransporter with 4-bromophenylalanine in Lipidic Cubic Phase

  • 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: 2.70 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.296 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.7 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: https://doi.org/10.1126/science.1261172
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Computationally Designed Transporter of Zn(II) and Proton26synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
4BF
Query on 4BF
A
L-PEPTIDE LINKINGC9 H10 Br N O2TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.296 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.87α = 90
b = 46.87β = 90
c = 60.603γ = 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 States7U01AI074571-05
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States3F32GM096727

Revision History  (Full details and data files)

  • 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: Advisory, 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
  • Version 1.6: 2023-12-27
    Changes: Advisory, Data collection, Database references
  • Version 1.7: 2024-03-27
    Changes: Refinement description