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- EMDB-62032: Cryo-EM structure of E coli pstSCAB in the resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-62032
TitleCryo-EM structure of E coli pstSCAB in the resting state
Map dataCryo-EM structure of E coli pstSCAB in the resting state
Sample
  • Complex: pstCAB
    • Protein or peptide: Phosphate transport system permease protein PstA
    • Protein or peptide: Phosphate transport system permease protein PstC
    • Protein or peptide: Phosphate import ATP-binding protein PstB
KeywordsABC transporter / Phosphate transport / pstSCAB complex / METAL TRANSPORT
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 / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / DNA damage response / ATP hydrolysis activity / ATP binding ...ABC-type phosphate transporter / ATPase-coupled phosphate ion transmembrane transporter activity / phosphate transmembrane transporter activity / phosphate ion transport / phosphate ion transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / 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. / 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. ...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. / 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 transport system permease protein PstA / Phosphate import ATP-binding protein PstB / Phosphate transport system permease protein PstC
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChen QF / Xiao H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071202 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, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62032.png

Downloads & links

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Map

FileDownload / File: emd_62032.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of E coli pstSCAB in the resting state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239
Minimum - Maximum-2.357915 - 3.8753772
Average (Standard dev.)0.0029156453 (±0.10426421)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62032_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62032_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pstCAB

EntireName: pstCAB
Components
  • Complex: pstCAB
    • Protein or peptide: Phosphate transport system permease protein PstA
    • Protein or peptide: Phosphate transport system permease protein PstC
    • Protein or peptide: Phosphate import ATP-binding protein PstB

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Supramolecule #1: pstCAB

SupramoleculeName: pstCAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Phosphate transport system permease protein PstA

MacromoleculeName: Phosphate transport system permease protein PstA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 32.346656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMVEMQTTA ALAESRRKMQ ARRRLKNRIA LTLSMATMAF GLFWLIWILM STITRGIDGM SLALFTEMTP PPNTEGGGLA NALAGSGLL ILWATVFGTP LGIMAGIYLA EYGRKSWLAE VIRFINDILL SAPSIVVGLF VYTIVVAQME HFSGWAGVIA L ALLQVPIV ...String:
MAMVEMQTTA ALAESRRKMQ ARRRLKNRIA LTLSMATMAF GLFWLIWILM STITRGIDGM SLALFTEMTP PPNTEGGGLA NALAGSGLL ILWATVFGTP LGIMAGIYLA EYGRKSWLAE VIRFINDILL SAPSIVVGLF VYTIVVAQME HFSGWAGVIA L ALLQVPIV IRTTENMLKL VPYSLREAAY ALGTPKWKMI SAITLKASVS GIMTGILLAI ARIAGETAPL LFTALSNQFW ST DMMQPIA NLPVTIFKFA MSPFAEWQQL AWAGVLIITL CVLLLNILAR VVFAKNKHG

UniProtKB: Phosphate transport system permease protein PstA

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Macromolecule #2: Phosphate transport system permease protein PstC

MacromoleculeName: Phosphate transport system permease protein PstC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 34.138785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAATKPAFNP PGKKGDIIFS VLVKLAALIV LLMLGGIIVS LIISSWPSIQ KFGLAFLWTK EWDAPNDIYG ALVPIYGTLV TSFIALLIA VPVSFGIALF LTELAPGWLK RPLGIAIELL AAIPSIVYGM WGLFIFAPLF AVYFQEPVGN IMSNIPIVGA L FSGPAFGI ...String:
MAATKPAFNP PGKKGDIIFS VLVKLAALIV LLMLGGIIVS LIISSWPSIQ KFGLAFLWTK EWDAPNDIYG ALVPIYGTLV TSFIALLIA VPVSFGIALF LTELAPGWLK RPLGIAIELL AAIPSIVYGM WGLFIFAPLF AVYFQEPVGN IMSNIPIVGA L FSGPAFGI GILAAGVILA IMIIPYIAAV MRDVFEQTPV MMKESAYGIG CTTWEVIWRI VLPFTKNGVI GGIMLGLGRA LG ETMAVTF IIGNTYQLDS ASLYMPGNSI TSALANEFAE AESGLHVAAL MELGLILFVI TFIVLAASKF MIMRLAKNEG AR

UniProtKB: Phosphate transport system permease protein PstC

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Macromolecule #3: Phosphate import ATP-binding protein PstB

MacromoleculeName: Phosphate import ATP-binding protein PstB / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type phosphate transporter
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 29.06027 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSMVETAPSK IQVRNLNFYY GKFHALKNIN LDIAKNQVTA FIGPSGCGKS TLLRTFNKMF ELYPEQRAEG EILLDGDNIL TNSQDIALL RAKVGMVFQK PTPFPMSIYD NIAFGVRLFE KLSRADMDER VQWALTKAAL WNETKDKLHQ SGYSLSGGQQ Q RLCIARGI ...String:
MSMVETAPSK IQVRNLNFYY GKFHALKNIN LDIAKNQVTA FIGPSGCGKS TLLRTFNKMF ELYPEQRAEG EILLDGDNIL TNSQDIALL RAKVGMVFQK PTPFPMSIYD NIAFGVRLFE KLSRADMDER VQWALTKAAL WNETKDKLHQ SGYSLSGGQQ Q RLCIARGI AIRPEVLLLD EPCSALDPIS TGRIEELITE LKQDYTVVIV THNMQQAARC SDHTAFMYLG ELIEFSNTDD LF TKPAKKQ TEDYITGRYG

UniProtKB: Phosphate import ATP-binding protein PstB

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: CCP4 package / Number images used: 1194741
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9k3y:
Cryo-EM structure of E coli pstSCAB in the resting state

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