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- PDB-10tu: ArsB from L. ferriphilum bound to arsenite in inward-facing state... -

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Basic information

Entry
Database: PDB / ID: 10tu
TitleArsB from L. ferriphilum bound to arsenite in inward-facing state (parallel 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 / TRIHYDROXYARSENITE(III) / Arsenical pump membrane protein
Function and homology information
Biological speciesLeptospirillum ferriphilum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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: To Be Published
Title: Structural basis of metalloid transport by the arsenite efflux pump ArsB
Authors: Mahajan, S. / Demirer, K. / Clemons, W.M. / Rees, D.C.
History
DepositionFeb 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,4174
Polymers94,1652
Non-polymers2522
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
#2: Chemical ChemComp-TAS / TRIHYDROXYARSENITE(III)


Mass: 125.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AsH3O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: #1 / 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 / Details: with 2 mM arsenite
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
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37353 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0086556
ELECTRON MICROSCOPYf_angle_d0.5948976
ELECTRON MICROSCOPYf_dihedral_angle_d4.129902
ELECTRON MICROSCOPYf_chiral_restr0.0431128
ELECTRON MICROSCOPYf_plane_restr0.0061084

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