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- EMDB-38935: Cryo-EM structure of E.coli spermidine transporter PotD-PotABC in... -

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Basic information

Entry
Database: EMDB / ID: EMD-38935
TitleCryo-EM structure of E.coli spermidine transporter PotD-PotABC in pre-translocation state
Map data
Sample
  • Complex: ABC transporter
    • Protein or peptide: Spermidine/putrescine import ATP-binding protein PotA
    • Protein or peptide: Spermidine/putrescine ABC transporter membrane protein
    • Protein or peptide: Spermidine/putrescine transport system permease protein PotC
    • Protein or peptide: Spermidine/putrescine-binding periplasmic protein
  • Ligand: SPERMIDINE
  • Ligand: water
KeywordsABC transporter / TRANSPORT PROTEIN
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/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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsQiao Z / Gao YG
Funding support Singapore, 1 items
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, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38935.png

Downloads & links

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Map

FileDownload / File: emd_38935.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 200 pix.
= 243.2 Å		1.22 Å/pix.
x 200 pix.
= 243.2 Å		1.22 Å/pix.
x 200 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.216 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.039
Minimum - Maximum-0.0017213287 - 1.9185708
Average (Standard dev.)0.0021624304 (±0.034751017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38935_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38935_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ABC transporter

EntireName: ABC transporter
Components
  • Complex: ABC transporter
    • Protein or peptide: Spermidine/putrescine import ATP-binding protein PotA
    • Protein or peptide: Spermidine/putrescine ABC transporter membrane protein
    • Protein or peptide: Spermidine/putrescine transport system permease protein PotC
    • Protein or peptide: Spermidine/putrescine-binding periplasmic protein
  • Ligand: SPERMIDINE
  • Ligand: water

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Supramolecule #1: ABC transporter

SupramoleculeName: ABC transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 186.1 kDa/nm

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

MacromoleculeName: Spermidine/putrescine import ATP-binding protein PotA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.079137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGQSKKLNKQ PSSLSPLVQL AGIRKCFDGK EVIPQLDLTI NNGEFLTLLG PSGCGKTTVL RLIAGLETVD SGRIMLDNED ITHVPAENR YVNTVFQSYA LFPHMTVFEN VAFGLRMQKT PAAEITPRVM EALRMVQLET FAQRKPHQLS GGQQQRVAIA R AVVNKPRL ...String:
MGQSKKLNKQ PSSLSPLVQL AGIRKCFDGK EVIPQLDLTI NNGEFLTLLG PSGCGKTTVL RLIAGLETVD SGRIMLDNED ITHVPAENR YVNTVFQSYA LFPHMTVFEN VAFGLRMQKT PAAEITPRVM EALRMVQLET FAQRKPHQLS GGQQQRVAIA R AVVNKPRL LLLDQSLSAL DYKLRKQMQN ELKALQRKLG ITFVFVTHDQ EEALTMSDRI VVMRDGRIEQ DGTPREIYEE PK NLFVAGF IGEINMFNAT VIERLDEQRV RANVEGRECN IYVNFAVEPG QKLHVLLRPE DLRVEEINDD NHAEGLIGYV RER NYKGMT LESVVELENG KMVMVSEFFN EDDPDFDHSL DQKMAINWVE SWEVVLADEE HK

UniProtKB: Spermidine/putrescine import ATP-binding protein PotA

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Macromolecule #2: Spermidine/putrescine ABC transporter membrane protein

MacromoleculeName: Spermidine/putrescine ABC transporter membrane protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 32.234164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKNTSKFQNV VIVTIVGWLV LFVFLPNLMI IGTSFLTRDD ASFVKMVFTL DNYTRLLDPL YFEVLLHSLN MALIATLACL VLGYPFAWF LAKLPHKVRP LLLFLLIVPF WTNSLIRIYG LKIFLSTKGY LNEFLLWLGV IDTPIRIMFT PSAVIIGLVY I LLPFMVMP ...String:
MKNTSKFQNV VIVTIVGWLV LFVFLPNLMI IGTSFLTRDD ASFVKMVFTL DNYTRLLDPL YFEVLLHSLN MALIATLACL VLGYPFAWF LAKLPHKVRP LLLFLLIVPF WTNSLIRIYG LKIFLSTKGY LNEFLLWLGV IDTPIRIMFT PSAVIIGLVY I LLPFMVMP LYSSIEKLDK PLLEAARDLG ASKLQTFIRI IIPLTMPGII AGCLLVMLPA MGLFYVSDLM GGAKNLLIGN VI KVQFLNI RDWPFGAATS ITLTIVMGLM LLVYWRASRL LNKKVELE

UniProtKB: Spermidine/putrescine ABC transporter membrane protein

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Macromolecule #3: Spermidine/putrescine transport system permease protein PotC

MacromoleculeName: Spermidine/putrescine transport system permease protein PotC
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.13285 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIGRLLRGGF MTAIYAYLYI PIIILIVNSF NSSRFGINWQ GFTTKWYSLL MNNDSLLQAA QHSLTMAVFS ATFATLIGSL TAVALYRYR FRGKPFVSGM LFVVMMSPDI VMAISLLVLF MLLGIQLGFW SLLFSHITFC LPFVVVTVYS RLKGFDVRML E AAKDLGAS ...String:
MIGRLLRGGF MTAIYAYLYI PIIILIVNSF NSSRFGINWQ GFTTKWYSLL MNNDSLLQAA QHSLTMAVFS ATFATLIGSL TAVALYRYR FRGKPFVSGM LFVVMMSPDI VMAISLLVLF MLLGIQLGFW SLLFSHITFC LPFVVVTVYS RLKGFDVRML E AAKDLGAS EFTILRKIIL PLAMPAVAAG WVLSFTLSMD DVVVSSFVTG PSYEILPLKI YSMVKVGVSP EVNALATILL VL SLVMVIA SQLIARDKTK GNTGDVK

UniProtKB: Spermidine/putrescine transport system permease protein PotC

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Macromolecule #4: Spermidine/putrescine-binding periplasmic protein

MacromoleculeName: Spermidine/putrescine-binding periplasmic protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 38.906938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKWSRHLLA AGALALGMSA AHADDNNTLY FYNWTEYVPP GLLEQFTKET GIKVIYSTYE SNETMYAKLK TYKDGAYDLV VPSTYYVDK MRKEGMIQKI DKSKLTNFSN LDPDMLNKPF DPNNDYSIPY IWGATAIGVN GDAVDPKSVT SWADLWKPEY K GSLLLTDD ...String:
MKKWSRHLLA AGALALGMSA AHADDNNTLY FYNWTEYVPP GLLEQFTKET GIKVIYSTYE SNETMYAKLK TYKDGAYDLV VPSTYYVDK MRKEGMIQKI DKSKLTNFSN LDPDMLNKPF DPNNDYSIPY IWGATAIGVN GDAVDPKSVT SWADLWKPEY K GSLLLTDD AREVFQMALR KLGYSGNTTD PKEIEAAYNE LKKLMPNVAA FNSDNPANPY MEGEVNLGMI WNGSAFVARQ AG TPIDVVW PKEGGIFWMD SLAIPANAKN KEGALKLINF LLRPDVAKQV AETIGYPTPN LAARKLLSPE VANDKTLYPD AET IKNGEW QNDVGAASSI YEEYYQKLKA GR

UniProtKB: Spermidine/putrescine-binding periplasmic protein

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Macromolecule #5: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration10 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61273
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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