28PB | pdb_000028pb

Crystal structure of CbcA periplasmic domain from Geobacter sulfurreducens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Bridging inner membrane and periplasm in Geobacter sulfurreducens: structural and biochemical insights into CbcA and its redox partners.

Antunes, J.M.A.Silva, M.A.Correia, M.A.S.Salgueiro, C.A.Santos-Silva, T.Morgado, L.

(2026) Int J Biol Macromol 369: 152597-152597

  • DOI: https://doi.org/10.1016/j.ijbiomac.2026.152597
  • Primary Citation Related Structures: 
    28PB

  • PubMed Abstract: 

    Biotechnological applications such as bioremediation, bioenergy production, and microbial electrosynthesis are emerging as sustainable alternatives to conventional and environmentally harmful industrial practices. Advancing these technologies requires a deeper understanding of extracellular electron transfer, a process mediated by a network of redox partners bridging the inner membrane and the extracellular environment in electroactive bacteria. The CbcBA complex, a quinol:cytochrome c oxidoreductase from Geobacter sulfurreducens, is essential for the reduction of extracellular metal oxides and electrodes with redox potential values below -210 mV. The complex comprises CbcA, a heptaheme c-type cytochrome anchored to the inner membrane and CbcB, an integral membrane di-heme b-type cytochrome. Additionally, CbcC, a periplasmic dodecaheme cytochrome, and the five periplasmic triheme cytochromes PpcA-E, are proposed to function as redox partners of CbcBA. To investigate their structural and functional properties, the periplasmic domain of CbcA (CbcA sol ) and CbcC were heterologously expressed and analyzed using complementary spectroscopic techniques. The crystal structure of CbcA sol was solved at 1.9 Å resolution, revealing a calcium-binding EF-hand motif that may function as a regulatory switch. Circular dichroism and differential scanning calorimetry indicated that CbcA sol and CbcC exhibit high stability, while potentiometric redox titrations demonstrated distinct electrochemical behaviors: CbcA sol has the most negative reduction potential among G. sulfurreducens oxidoreductases, whereas CbcC operates within the redox range of the PpcA-E cytochromes. NMR experiments showed that CbcA sol transfers electrons to CbcC and PpcA-E cytochromes. This result, in agreement with the structural electrostatic complementarity between the different cytochromes, suggests that CbcA may interact with multiple periplasmic cytochromes through distinct surface regions.


  • Organizational Affiliation
    • Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.

Macromolecule Content 

  • Total Structure Weight: 69.98 kDa 
  • Atom Count: 5,184 
  • Modeled Residue Count: 554 
  • Deposited Residue Count: 556 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c
A, B
278Geobacter sulfurreducens PCAMutation(s): 0 
Gene Names: GSU0594
UniProt
Find proteins for Q74FL3 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Explore Q74FL3 
Go to UniProtKB:  Q74FL3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ74FL3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC

Query on HEC



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
R [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
S [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.436α = 90
b = 94.167β = 90
c = 114.175γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugal2022.11900.BD
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04378/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/04378/2020
Fundacao para a Ciencia e a TecnologiaPortugalLA/P/0140/2020
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BIA-BQM/4967/2020
Fundacao para a Ciencia e a TecnologiaPortugalEXPL/BIA-BQM/0770/2021

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Database references
  • Version 1.2: 2026-06-10
    Changes: Database references