7KYO

PsaBC from Streptococcus pneumoniae in complex with Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

The structural basis of bacterial manganese import.

Neville, S.L., Sjohamn, J., Watts, J.A., MacDermott-Opeskin, H., Fairweather, S.J., Ganio, K., Carey Hulyer, A., McGrath, A.P., Hayes, A.J., Malcolm, T.R., Davies, M.R., Nomura, N., Iwata, S., O'Mara, M.L., Maher, M.J., McDevitt, C.A.

(2021) Sci Adv 7

  • DOI: 10.1126/sciadv.abg3980
  • Primary Citation of Related Structures:  
    7KYO, 7KYP

  • PubMed Abstract: 

    • Metal ions are essential for all forms of life. In prokaryotes, ATP-binding cassette (ABC) permeases serve as the primary import pathway for many micronutrients including the first-row transition metal manganese. However, the structural features of ionic metal transporting ABC permeases have remained undefined ...

    Metal ions are essential for all forms of life. In prokaryotes, ATP-binding cassette (ABC) permeases serve as the primary import pathway for many micronutrients including the first-row transition metal manganese. However, the structural features of ionic metal transporting ABC permeases have remained undefined. Here, we present the crystal structure of the manganese transporter PsaBC from Streptococcus pneumoniae in an open-inward conformation. The type II transporter has a tightly closed transmembrane channel due to "extracellular gating" residues that prevent water permeation or ion reflux. Below these residues, the channel contains a hitherto unreported metal coordination site, which is essential for manganese translocation. Mutagenesis of the extracellular gate perturbs manganese uptake, while coordination site mutagenesis abolishes import. These structural features are highly conserved in metal-specific ABC transporters and are represented throughout the kingdoms of life. Collectively, our results define the structure of PsaBC and reveal the features required for divalent cation transport.

    Organizational Affiliation: 

    Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia. megan.maher@unimelb.edu.au christopher.mcdevitt@unimelb.edu.au.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Manganese ABC transporter, ATP-binding proteinA [auth B]240Streptococcus pneumoniae D39Mutation(s): 0 
Gene Names: psaB, SPD_1461
UniProt
Find proteins for A0A0H2ZNF3 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore A0A0H2ZNF3 
Go to UniProtKB:  A0A0H2ZNF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZNF3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab heavy chainB [auth H]234Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chainC [auth L]218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Manganese ABC transporter, permease proteinD [auth C]282Streptococcus pneumoniae D39Mutation(s): 0 
Gene Names: psaC, SPD_1462
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H2ZPI2 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore A0A0H2ZPI2 
Go to UniProtKB:  A0A0H2ZPI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZPI2
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.66α = 90
b = 241.7β = 90
c = 98.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1080784
National Health and Medical Research Council (NHMRC, Australia)Australia1140554
National Health and Medical Research Council (NHMRC, Australia)Australia1122582
Australian Research Council (ARC)AustraliaDP170102102
Australian Research Council (ARC)AustraliaFT170100006
Australian Research Council (ARC)AustraliaFT180100397
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101079

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release