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- PDB-9k3x: Cryo-EM structure of E coli pstSCAB in the pretranslocation state -

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Basic information

Entry
Database: PDB / ID: 9k3x
TitleCryo-EM structure of E coli pstSCAB in the pretranslocation state
Components
  • Phosphate import ATP-binding protein PstB
  • Phosphate transport system permease protein PstA
  • Phosphate transport system permease protein PstC
  • Phosphate-binding protein PstS
KeywordsMETAL TRANSPORT / ABC transporter / Phosphate transport / pstSCAB complex
Function / homology
Function and homology information


ABC-type phosphate transporter / ATPase-coupled phosphate ion transmembrane transporter activity / phosphate transmembrane transporter activity / phosphate ion transport / phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / outer membrane-bounded periplasmic space / DNA damage response ...ABC-type phosphate transporter / ATPase-coupled phosphate ion transmembrane transporter activity / phosphate transmembrane transporter activity / phosphate ion transport / phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / outer membrane-bounded periplasmic space / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Phosphate transport system permease protein 1 / Phosphate transport system permease protein PstA / Phosphate ABC transporter, permease protein PstC / : / : / Phosphate import ATP-binding protein pstB family profile. / Phosphate ABC transporter, substrate-binding protein PstS / : / PBP domain / PBP superfamily domain ...Phosphate transport system permease protein 1 / Phosphate transport system permease protein PstA / Phosphate ABC transporter, permease protein PstC / : / : / Phosphate import ATP-binding protein pstB family profile. / Phosphate ABC transporter, substrate-binding protein PstS / : / PBP domain / PBP superfamily domain / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Phosphate transport system permease protein PstA / Phosphate import ATP-binding protein PstB / Phosphate-binding protein PstS / Phosphate transport system permease protein PstC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsChen, Q.F. / Xiao, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071202 China
National Natural Science Foundation of China (NSFC)32371261 China
CitationJournal: Nat Commun / Year: 2026
Title: Molecular mechanism of phosphate import by the bacterial PstSCAB transporter.
Authors: Hu Xiao / Shanqin Li / Ruxi Qi / Yuxiang Hu / Xiaozi Jiang / Jing Luo / Jing Wu / Lei Zhang / Shuman Xu / Defen Lu / Xinwang Yang / Qingfeng Chen / Sheng Liu /
Abstract: Inorganic phosphate (Pi) is essential for all living organisms. PstSCAB, a bacterial high-affinity ABC transporter, imports Pi under limiting conditions via five subunits: PstA and PstC forming the ...Inorganic phosphate (Pi) is essential for all living organisms. PstSCAB, a bacterial high-affinity ABC transporter, imports Pi under limiting conditions via five subunits: PstA and PstC forming the transmembrane domain (TMD), periplasmic PstS that switches between free and TMD-docked forms for Pi capture and delivery, and two cytosolic PstB subunits for ATP binding and hydrolysis. Its malfunction affects the virulence of pathogenic bacteria, making it pharmaceutically attractive. However, complete structural pictures of PstSCAB in different states remain lacking. Here, we determine cryo-EM structures of PstSCAB in resting, pretranslocation, and catalytic intermediate states, which reveal that conformational changes in PstS and ATP binding/unbinding in PstB collectively induce rigid-body movements of TMD, generating inward- or outward-facing conformations. In TMD, Pi specificity is determined by positively charged Arg220 (PstA) and Arg237 (PstC). This study advances understanding of bacterial Pi import and supports drug development targeting PstSCAB.
History
DepositionOct 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Phosphate transport system permease protein PstA
B: Phosphate transport system permease protein PstC
C: Phosphate import ATP-binding protein PstB
D: Phosphate import ATP-binding protein PstB
E: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6886
Polymers161,5935
Non-polymers951
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 Phosphate transport system permease protein PstA


Mass: 32320.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pstA, phoT, b3726, JW3704 / Production host: Escherichia coli (E. coli) / References: UniProt: P07654
#2: Protein Phosphate transport system permease protein PstC


Mass: 34126.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pstC, phoW, b3727, JW3705 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGH8
#3: Protein Phosphate import ATP-binding protein PstB / ABC phosphate transporter / Phosphate-transporting ATPase


Mass: 29060.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pstB, phoT, b3725, JW3703 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAH0, ABC-type phosphate transporter
#4: Protein Phosphate-binding protein PstS / PBP


Mass: 37024.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pstS, phoS, b3728, JW3706 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG82
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / 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: pstSCAB_4CYS / Type: COMPLEX
Details: Cryo-EM structure of E coli pstSCAB in the pretranslocation state
Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.158 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1CTFFINDparticle selection
13CCP4 package3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 787966 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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