4P6K

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

  • Classification: DE NOVO PROTEIN

  • 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; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.704 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Computationally Designed Transporter of Zn(II) and Proton
A
26N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A
NON-POLYMERH2 N

--

4BF
Query on 4BF
A
L-PEPTIDE LINKINGC9 H10 Br N O2TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.704 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.295 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 46.870α = 90.00
b = 46.870β = 90.00
c = 60.603γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States7U01AI074571-05
National Institutes of Health/National Institute of General Medical SciencesUnited States3F32GM096727

Revision History 

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