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- PDB-8y5h: Cryo-EM structure of E.coli spermidine transporter PotD-PotABC in... -

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Basic information

Entry
Database: PDB / ID: 8y5h
TitleCryo-EM structure of E.coli spermidine transporter PotD-PotABC in pre-translocation state
Components
  • (Spermidine/putrescine ...) x 3
  • Spermidine/putrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / ABC transporter
Function / homology
Function and homology information


ABC-type polyamine transporter / ABC-type putrescine transporter activity / spermidine transmembrane transport / spermidine binding / spermidine transport / putrescine binding / putrescine transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space ...ABC-type polyamine transporter / ABC-type putrescine transporter activity / spermidine transmembrane transport / spermidine binding / spermidine transport / putrescine binding / putrescine transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Spermidine/putrescine ABC transporter, ATP-binding subunit / PotA, ATP-binding domain / : / : / Spermidine/putrescine-binding periplasmic protein / Transport-associated OB, type 2 / TOBE domain / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily ...Spermidine/putrescine ABC transporter, ATP-binding subunit / PotA, ATP-binding domain / : / : / Spermidine/putrescine-binding periplasmic protein / Transport-associated OB, type 2 / TOBE domain / Molybdate/tungstate binding, C-terminal / 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. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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
SPERMIDINE / Spermidine/putrescine ABC transporter membrane protein / Spermidine/putrescine import ATP-binding protein PotA / Spermidine/putrescine transport system permease protein PotC / Spermidine/putrescine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsQiao, Z. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Sci Adv / Year: 2024
Title: Structural insights into polyamine spermidine uptake by the ABC transporter PotD-PotABC.
Authors: Zhu Qiao / Phong Hoa Do / Joshua Yi Yeo / Rya Ero / Zhuowen Li / Liying Zhan / Sandip Basak / Yong-Gui Gao /
Abstract: Polyamines, characterized by their polycationic nature, are ubiquitously present in all organisms and play numerous cellular functions. Among polyamines, spermidine stands out as the predominant type ...Polyamines, characterized by their polycationic nature, are ubiquitously present in all organisms and play numerous cellular functions. Among polyamines, spermidine stands out as the predominant type in both prokaryotic and eukaryotic cells. The PotD-PotABC protein complex in , belonging to the adenosine triphosphate-binding cassette transporter family, is a spermidine-preferential uptake system. Here, we report structural details of the polyamine uptake system PotD-PotABC in various states. Our analyses reveal distinct "inward-facing" and "outward-facing" conformations of the PotD-PotABC transporter, as well as conformational changes in the "gating" residues (F222, Y223, D226, and K241 in PotB; Y219 and K223 in PotC) controlling spermidine uptake. Therefore, our structural analysis provides insights into how the PotD-PotABC importer recognizes the substrate-binding protein PotD and elucidates molecular insights into the spermidine uptake mechanism of bacteria.
History
DepositionJan 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spermidine/putrescine import ATP-binding protein PotA
B: Spermidine/putrescine ABC transporter membrane protein
C: Spermidine/putrescine transport system permease protein PotC
D: Spermidine/putrescine import ATP-binding protein PotA
E: Spermidine/putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,5776
Polymers186,4325
Non-polymers1451
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Spermidine/putrescine ... , 3 types, 4 molecules ADBC

#1: Protein Spermidine/putrescine import ATP-binding protein PotA


Mass: 43079.137 Da / Num. of mol.: 2 / Mutation: E173Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: potA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q6AZ03
#2: Protein Spermidine/putrescine ABC transporter membrane protein


Mass: 32234.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: potB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y861
#3: Protein Spermidine/putrescine transport system permease protein PotC


Mass: 29132.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: potC / Production host: Escherichia coli (E. coli) / References: UniProt: C3TDI7

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Protein , 1 types, 1 molecules E

#4: Protein Spermidine/putrescine-binding periplasmic protein / SPBP


Mass: 38906.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: potD, b1123, JW1109 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFK9

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: ABC transporter / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 186.1 kDa/nm / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 10 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61273 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00712660
ELECTRON MICROSCOPYf_angle_d0.76317175
ELECTRON MICROSCOPYf_dihedral_angle_d8.4551691
ELECTRON MICROSCOPYf_chiral_restr0.0511978
ELECTRON MICROSCOPYf_plane_restr0.0072181

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