8Y5I

Cryo-EM structure of E.coli spermidine transporter PotD-PotABC in translocation intermidiate state

PDB DOI: https://doi.org/10.2210/pdb8Y5I/pdb
EM Map EMD-38936: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2024-01-31 Released: 2024-10-09
Deposition Author(s): Qiao, Z., Gao, Y.G.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into polyamine spermidine uptake by the ABC transporter PotD-PotABC.

Qiao, Z., Do, P.H., Yeo, J.Y., Ero, R., Li, Z., Zhan, L., Basak, S., Gao, Y.G.

(2024) Sci Adv 10: eado8107-eado8107

PubMed: 39303029 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.ado8107
Primary Citation of Related Structures:
8Y5F, 8Y5G, 8Y5H, 8Y5I, 8ZX1

PubMed 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 in both prokaryotic and eukaryotic cells. The PotD-PotABC protein complex in Escherichia coli , 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.

Organizational Affiliation

School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.

Macromolecule Content

Total Structure Weight: 187.47 kDa
Atom Count: 12,374
Modelled Residue Count: 1,553
Deposited Residue Count: 1,653
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine/putrescine import ATP-binding protein PotA	A, D	378	Escherichia coli	Mutation(s): 1 Gene Names: potA, b1126, JW1112 EC: 7.6.2.11 Membrane Entity: Yes
UniProt
Find proteins for P69874 (Escherichia coli (strain K12)) Explore P69874 Go to UniProtKB: P69874
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69874
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine/putrescine transport system permease protein PotB	B	285	Escherichia coli	Mutation(s): 0 Gene Names: potB, b1125, JW1111
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine/putrescine transport system permease protein PotC	C	264	Escherichia coli	Mutation(s): 0 Gene Names: potC, b1124, JW1110 Membrane Entity: Yes
UniProt
Find proteins for P0AFK6 (Escherichia coli (strain K12)) Explore P0AFK6 Go to UniProtKB: P0AFK6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AFK6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Putrescine-binding periplasmic protein	E	348	Escherichia coli	Mutation(s): 0 Gene Names: potD, potD_1, A9X72_15260, AC065_02235, ACN81_08960, ACU57_04395, AM464_23650, BF481_002097, BGM66_002097, BJI68_20810... potD, potD_1, A9X72_15260, AC065_02235, ACN81_08960, ACU57_04395, AM464_23650, BF481_002097, BGM66_002097, BJI68_20810, BJJ90_15605, BMT50_26180, BMT91_12660, BvCmsSIP010_04197, C0P57_004320, C1Q91_003201, C5N07_18640, CA593_22865, CCS08_25895, CF22_003053, CG692_05805, CG831_001508, CQ986_001050, CR538_15460, CR539_10310, CTR35_002408, CV83915_00461, D9H94_04145, DIV22_29210, DN627_23510, DS732_10680, DTL43_16095, E0I52_23195, E4K51_18510, E5H86_12360, E6D34_10765, EAN77_25155, ECs1499, EIZ93_12980, ERS139208_03585, F3P10_09120, FFF58_15800, FHD44_11245, FJQ40_01110, FN993_001405, FOI11_007330, FOI11_14300, FPS11_22525, FV293_24150, G3V95_08220, G4A38_16220, G4A47_15580, GIB53_10955, GJ11_06750, GKF89_00455, GNW61_10810, GOP14_002871, GOP25_17235, GP965_23750, GQM17_13980, GQM21_19780, GQN34_10415, GRW56_11575, GRW56_16830, H0P11_10030, HHH44_002984, HLQ92_15565, HMV95_16200, HV209_29265, HVY77_15605, HX136_15480, I6H00_08380, I6H02_24690, J0541_003203, J4S20_003291, J5U05_002927, JFD_02102, JNP96_10880, NCTC10090_00712, NCTC10865_03647, NCTC11127_00497, NCTC11181_00132, NCTC11341_04942, NCTC4450_04159, NCTC8960_00797, NCTC8985_01697, NCTC9071_02742, NCTC9706_00378, NEP60_22980, RG28_17065, SAMEA3472044_03468, SAMEA3752557_01589, SAMEA3753106_00760 Membrane Entity: Yes
UniProt
Find proteins for C3TDJ2 (Escherichia coli) Explore C3TDJ2 Go to UniProtKB: C3TDJ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3TDJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D]	F [auth A], H [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth D]	G [auth A], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth D]