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- PDB-9nbo: Closed conformation of ArsA from L. ferriphilum in complex with M... -

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Basic information

Entry
Database: PDB / ID: 9nbo
TitleClosed conformation of ArsA from L. ferriphilum in complex with MgATP and arsenite
ComponentsArsenite transporter ATPase-like protein,arsA
KeywordsHYDROLASE / ATPase / closed conformation / closed state / arsenite / arsenic / ATP / Intradimeric Walker A
Function / homology
Function and homology information


arsenite-transporting ATPase / ATPase-coupled arsenite transmembrane transporter activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
Arsenical pump-driving ATPase / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ARSENIC / ADENOSINE-5'-TRIPHOSPHATE / arsenite-transporting ATPase
Similarity search - Component
Biological speciesLeptospirillum ferriphilum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMahajan, S. / Li, Y.E. / Rees, D.C. / Clemons, W.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Nucleotide- and metalloid-driven conformational changes in the arsenite efflux ATPase ArsA
Authors: Mahajan, S. / Pall, A.E. / Li, Y.E. / Stemmler, T.L. / Rees, D.C. / Clemons Jr., W.M.
History
DepositionFeb 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arsenite transporter ATPase-like protein,arsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1086
Polymers63,9701
Non-polymers1,1385
Water905
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 Arsenite transporter ATPase-like protein,arsA


Mass: 63970.035 Da / Num. of mol.: 1 / Mutation: D46N,D364N
Source method: isolated from a genetically manipulated source
Details: non-hydrolyzing mutant / Source: (gene. exp.) Leptospirillum ferriphilum (bacteria) / Strain: ML-04 / Gene: LFML04_2459 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9ZFA3
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: ArsA closed state in complex with MgATP and arsenite / Type: COMPLEX
Details: ArsA incubated with 2 mM each of MgCl2, ATP and sodium arsenite for 30 min
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Leptospirillum ferriphilum (bacteria) / Strain: ML-04
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: ArsA incubated with 2 mM each of MgCl2, ATP and sodium arsenite for 30 min
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: 2500 nm / Nominal defocus min: 500 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 softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91645 / Symmetry type: POINT

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