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- EMDB-38934: Cryo-EM structure of E.coli spermidine transporter PotABC with sp... -

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Basic information

Entry
Database: EMDB / ID: EMD-38934
TitleCryo-EM structure of E.coli spermidine transporter PotABC with spermidine
Map data
Sample
  • Complex: ABC transporter
    • Protein or peptide: Spermidine/putrescine import ATP-binding protein PotA
    • Protein or peptide: Spermidine/putrescine ABC transporter permease PotB
    • Protein or peptide: Spermidine/putrescine transport system permease protein PotC
  • Protein or peptide: Spermidine/putrescine import ATP-binding protein PotA
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE
KeywordsABC transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type polyamine transporter / ABC-type putrescine transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Spermidine/putrescine ABC transporter, ATP-binding subunit / PotA, ATP-binding domain / : / : / 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 ...Spermidine/putrescine ABC transporter, ATP-binding subunit / PotA, ATP-binding domain / : / : / 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. / 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 import ATP-binding protein PotA / Spermidine/putrescine ABC transporter permease PotB / Spermidine/putrescine transport system permease protein PotC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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_38934.png

Downloads & links

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Map

FileDownload / File: emd_38934.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 256 pix.
= 194.56 Å		0.76 Å/pix.
x 256 pix.
= 194.56 Å		0.76 Å/pix.
x 256 pix.
= 194.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0612
Minimum - Maximum-0.0017399484 - 1.8998345
Average (Standard dev.)0.0032244886 (±0.042121124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 194.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38934_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_38934_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 permease PotB
    • Protein or peptide: Spermidine/putrescine transport system permease protein PotC
  • Protein or peptide: Spermidine/putrescine import ATP-binding protein PotA
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE

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Supramolecule #1: ABC transporter

SupramoleculeName: ABC transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 147.3 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: 1 / Enantiomer: LEVO / EC number: ABC-type polyamine transporter
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 41.022773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SPLVQLAGIR KCFDGKEVIP QLDLTINNGE FLTLLGPSGC GKTTVLRLIA GLETVDSGRI MLDNEDITHV PAENRYVNTV FQSYALFPH MTVFENVAFG LRMQKTPAAE ITPRVMEALR MVQLETFAQR KPHQLSGGQQ QRVAIARAVV NKPRLLLLDQ S LSALDYKL ...String:
SPLVQLAGIR KCFDGKEVIP QLDLTINNGE FLTLLGPSGC GKTTVLRLIA GLETVDSGRI MLDNEDITHV PAENRYVNTV FQSYALFPH MTVFENVAFG LRMQKTPAAE ITPRVMEALR MVQLETFAQR KPHQLSGGQQ QRVAIARAVV NKPRLLLLDQ S LSALDYKL RKQMQNELKA LQRKLGITFV FVTHDQEEAL TMSDRIVVMR DGRIEQDGTP REIYEEPKNL FVAGFIGEIN MF NATVIER LDEQRVRANV EGRECNIYVN FAVEPGQKLH VLLRPEDLRV EEINDDNHAE GLIGYVRERN YKGMTLESVV ELE NGKMVM VSEFFNEDDP DFDHSLDQKM AINWVESWEV VLAD

UniProtKB: Spermidine/putrescine import ATP-binding protein PotA

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Macromolecule #2: Spermidine/putrescine ABC transporter permease PotB

MacromoleculeName: Spermidine/putrescine ABC transporter permease PotB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.813455 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FQNVVIVTIV GWLVLFVFLP NLMIIGTSFL TRDDASFVKM VFTLDNYTRL LDPLYFEVLL HSLNMALIAT LACLVLGYPF AWFLAKLPH KVRPLLLFLL IVPFWTNSLI RIYGLKIFLS TKGYLNEFLL WLGVIDTPIR IMFTPSAVII GLVYILLPFM V MPLYSSIE ...String:
FQNVVIVTIV GWLVLFVFLP NLMIIGTSFL TRDDASFVKM VFTLDNYTRL LDPLYFEVLL HSLNMALIAT LACLVLGYPF AWFLAKLPH KVRPLLLFLL IVPFWTNSLI RIYGLKIFLS TKGYLNEFLL WLGVIDTPIR IMFTPSAVII GLVYILLPFM V MPLYSSIE KLDKPLLEAA RDLGASKLQT FIRIIIPLTM PGIIAGCLLV MLPAMGLFYV SDLMGGAKNL LIGNVIKVQF LN IRDWPFG AATSITLTIV MGLMLLVYWR ASRLLN

UniProtKB: Spermidine/putrescine ABC transporter permease PotB

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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: 27.526998 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LLRGGFMTAI YAYLYIPIII LIVNSFNSSR FGINWQGFTT KWYSLLMNND SLLQAAQHSL TMAVFSATFA TLIGSLTAVA LYRYRFRGK PFVSGMLFVV MMSPDIVMAI SLLVLFMLLG IQLGFWSLLF SHITFCLPFV VVTVYSRLKG FDVRMLEAAK D LGASEFTI ...String:
LLRGGFMTAI YAYLYIPIII LIVNSFNSSR FGINWQGFTT KWYSLLMNND SLLQAAQHSL TMAVFSATFA TLIGSLTAVA LYRYRFRGK PFVSGMLFVV MMSPDIVMAI SLLVLFMLLG IQLGFWSLLF SHITFCLPFV VVTVYSRLKG FDVRMLEAAK D LGASEFTI LRKIILPLAM PAVAAGWVLS FTLSMDDVVV SSFVTGPSYE ILPLKIYSMV KVGVSPEVNA LATILLVLSL VM VIASQLI AR

UniProtKB: Spermidine/putrescine transport system permease protein PotC

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Macromolecule #4: Spermidine/putrescine import ATP-binding protein PotA

MacromoleculeName: Spermidine/putrescine import ATP-binding protein PotA / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type polyamine transporter
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 40.820609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PLVQLAGIRK CFDGKEVIPQ LDLTINNGEF LTLLGPSGCG KTTVLRLIAG LETVDSGRIM LDNEDITHVP AENRYVNTVF QSYALFPHM TVFENVAFGL RMQKTPAAEI TPRVMEALRM VQLETFAQRK PHQLSGGQQQ RVAIARAVVN KPRLLLLDQS L SALDYKLR ...String:
PLVQLAGIRK CFDGKEVIPQ LDLTINNGEF LTLLGPSGCG KTTVLRLIAG LETVDSGRIM LDNEDITHVP AENRYVNTVF QSYALFPHM TVFENVAFGL RMQKTPAAEI TPRVMEALRM VQLETFAQRK PHQLSGGQQQ RVAIARAVVN KPRLLLLDQS L SALDYKLR KQMQNELKAL QRKLGITFVF VTHDQEEALT MSDRIVVMRD GRIEQDGTPR EIYEEPKNLF VAGFIGEINM FN ATVIERL DEQRVRANVE GRECNIYVNF AVEPGQKLHV LLRPEDLRVE EINDDNHAEG LIGYVRERNY KGMTLESVVE LEN GKMVMV SEFFNEDDPD FDHSLDQKMA INWVESWEVV LA

UniProtKB: Spermidine/putrescine import ATP-binding protein PotA

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

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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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98494
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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