4MKI | pdb_00004mki

Cobalt transporter ATP-binding subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.251 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural basis for a homodimeric ATPase subunit of an ECF transporter

Chai, C.L.Yu, Y.Zhuo, W.Zhao, H.Li, X.Wang, N.Chai, J.Yang, M.

(2013) Protein Cell 4: 793-801

  • DOI: https://doi.org/10.1007/s13238-013-3915-y
  • Primary Citation Related Structures: 
    4MKI

  • PubMed Abstract: 

    The transition metal cobalt, an essential cofactor for many enzymes in prokaryotes, is taken up by several specific transport systems. The CbiMNQO protein complex belongs to type-1 energy-coupling factor (ECF) transporters and is a widespread group of microbial cobalt transporters. CbiO is the ATPase subunit (A-component) of the cobalt transporting system in the gram-negative thermophilic bacterium Thermoanaerobacter tengcongensis. Here we report the crystal structure of a nucleotide-free CbiO at a resolution of 2.3 Å. CbiO contains an N-terminal canonical nucleotide-binding domain (NBD) and C-terminal helical domain. Structural and biochemical data show that CbiO forms a homodimer mediated by the NBD and the C-terminal domain. Interactions mainly via conserved hydrophobic amino acids between the two C-terminal domains result in formation of a four-helix bundle. Structural comparison with other ECF transporters suggests that non-conserved residues outside the T-component binding groove in the A component likely act as a specificity determinant for T components. Together, our data provide information on understanding of the structural organization and interaction of the CbiMNQO system.


  • Organizational Affiliation
    • College of Biological Sciences, China Agricultural University, Beijing, 100083, China.

Macromolecule Content 

  • Total Structure Weight: 68.7 kDa 
  • Atom Count: 4,728 
  • Modeled Residue Count: 568 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2A [auth B],
B [auth A]
298Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 0 
Gene Names: ecfA2cbiO2
EC: 3.6.3 (PDB Primary Data), 7 (UniProt)
UniProt
Find proteins for Q8R7Y5 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8R7Y5 
Go to UniProtKB:  Q8R7Y5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R7Y5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.229α = 90
b = 115.163β = 90
c = 54.416γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Structure summary
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description