4FI3

Structure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of AMP-PNP-bound vitamin B12 transporter BtuCD-F.

Korkhov, V.M.Mireku, S.A.Locher, K.P.

(2012) Nature 490: 367-372

  • DOI: 10.1038/nature11442
  • Primary Citation of Related Structures:  
    4FI3

  • PubMed Abstract: 
  • The ATP-binding cassette (ABC) transporter BtuCD mediates the uptake of vitamin B(12) across the inner membrane of Escherichia coli. Previous structures have shown the conformations of apo states, but the transport mechanism has remained unclear. Here we report the 3 ...

    The ATP-binding cassette (ABC) transporter BtuCD mediates the uptake of vitamin B(12) across the inner membrane of Escherichia coli. Previous structures have shown the conformations of apo states, but the transport mechanism has remained unclear. Here we report the 3.5 Å crystal structure of the transporter-binding protein complex BtuCD-BtuF (BtuCD-F) trapped in an β-γ-imidoadenosine 5'-phosphate (AMP-PNP)-bound intermediate state. Although the ABC domains (BtuD subunits) form the expected closed sandwich dimer, the membrane-spanning BtuC subunits adopt a new conformation, with the central translocation pathway sealed by a previously unrecognized cytoplasmic gate. A fully enclosed cavity is thus formed approximately halfway across the membrane. It is large enough to accommodate a vitamin B(12) molecule, and radioligand trapping showed that liposome-reconstituted BtuCD-F indeed contains bound B(12) in the presence of AMP-PNP. In combination with engineered disulphide crosslinking and functional assays, our data suggest an unexpected peristaltic transport mechanism that is distinct from those observed in other ABC transporters.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vitamin B12 import system permease protein BtuC AB349Escherichia coli K-12Mutation(s): 7 
Gene Names: btuCb1711JW1701
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
BtuCD-F Vitamin B12 Transporter with bound AMP-PNP
Find proteins for P06609 (Escherichia coli (strain K12))
Explore P06609 
Go to UniProtKB:  P06609
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vitamin B12 import ATP-binding protein BtuD CD249Escherichia coli K-12Mutation(s): 3 
Gene Names: btuDb1709JW1699
EC: 3.6.3.33 (PDB Primary Data), 7.6.2.8 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
BtuCD-F Vitamin B12 Transporter with bound AMP-PNP
Find proteins for P06611 (Escherichia coli (strain K12))
Explore P06611 
Go to UniProtKB:  P06611
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vitamin B12-binding protein F255Escherichia coli K-12Mutation(s): 0 
Gene Names: btuFyadTb0158JW0154
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
BtuCD-F Vitamin B12 Transporter with bound AMP-PNP
Find proteins for P37028 (Escherichia coli (strain K12))
Explore P37028 
Go to UniProtKB:  P37028
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.73α = 90
b = 211.99β = 90
c = 179.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXmodel building
PHENIXrefinement
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references