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- PDB-10tq: ArsB from L. ferriphilum in inward-facing state (antiparallel dimer) -

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Basic information

Entry
Database: PDB / ID: 10tq
TitleArsB from L. ferriphilum in inward-facing state (antiparallel dimer)
ComponentsArsenical pump membrane protein
KeywordsMEMBRANE PROTEIN / arsenite / membrane transporter / secondary transporter
Function / homologyarsenite secondary active transmembrane transporter activity / antimonite secondary active transmembrane transporter activity / Arsenical pump membrane protein, ArsB / Arsenical pump membrane protein / response to arsenic-containing substance / plasma membrane / Arsenical pump membrane protein
Function and homology information
Biological speciesLeptospirillum ferriphilum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMahajan, S. / Clemons, W.M. / Rees, D.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Chan Zuckerberg Initiative United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of metalloid transport by the arsenite efflux pump ArsB.
Authors: Shivansh Mahajan / Kemal Demirer / William M Clemons / Douglas C Rees /
Abstract: Bacteria resist toxic arsenite (As) in their environments by actively pumping the metalloid out of the cell via efflux pumps such as ArsB. However, the mechanism of extrusion remains poorly ...Bacteria resist toxic arsenite (As) in their environments by actively pumping the metalloid out of the cell via efflux pumps such as ArsB. However, the mechanism of extrusion remains poorly understood, which hinders the development of engineered bioremediation strategies. We report high-resolution cryo-EM structures of ArsB from the arsenic-tolerant bacterium Leptospirillum ferriphilum. ArsB adopts an inverted two-fold repeat architecture resembling that of other ion transporter (IT) superfamily proteins. Structures determined in the presence of arsenite and antimonite reveal that the metalloid substrates interact with polar residues at the core of the transmembrane domain primarily via hydrogen bonding. Mutagenesis and in vivo functional assays support these interactions. Our ArsB structures represent an 'inward-facing' conformation, where the metalloid-binding site is exposed to the cytoplasm, suitable for metalloid capture. Furthermore, we demonstrate that arsenite resistance conferred by ArsB varies with external pH, supporting that ArsB is a proton (H)-coupled secondary transporter. Mutagenesis, in vivo functional assays, and pK estimation imply that conserved aspartate residues near the metalloid-binding site likely mediate the H-coupling mechanism. Our findings provide structural insights into metalloid recognition and H/metalloid antiport in ArsB, laying a foundation for further elucidation of the molecular basis of toxic metalloid detoxification in bacteria.
History
DepositionFeb 8, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arsenical pump membrane protein
B: Arsenical pump membrane protein


Theoretical massNumber of molelcules
Total (without water)94,1652
Polymers94,1652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Arsenical pump membrane protein


Mass: 47082.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospirillum ferriphilum (bacteria) / Strain: ML-04 / Gene: LFML04_2457 / Production host: Escherichia coli (E. coli) / Strain (production host): Nico21(DE3) / References: UniProt: J9ZEP4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ArsB in inward-facing state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Leptospirillum ferriphilum (bacteria) / Strain: ML-04
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Nico21(DE3)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57278 / Symmetry type: POINT

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