8Y5G

Cryo-EM structure of E.coli spermidine transporter PotABC with spermidine

PDB DOI: https://doi.org/10.2210/pdb8Y5G/pdb
EM Map EMD-38934: 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: 140.43 kDa
Atom Count: 9,860
Modelled Residue Count: 1,240
Deposited Residue Count: 1,240
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	360	Escherichia coli	Mutation(s): 1 Gene Names: potA, C2M16_24850 EC: 7.6.2.11 Membrane Entity: Yes
UniProt
Find proteins for A0A2K3TLI6 (Escherichia coli) Explore A0A2K3TLI6 Go to UniProtKB: A0A2K3TLI6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K3TLI6
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 ABC transporter permease PotB	B	273	Escherichia coli	Mutation(s): 0 Gene Names: potB, EAI46_21425 Membrane Entity: Yes
UniProt
Find proteins for A0A3L9I213 (Escherichia coli) Explore A0A3L9I213 Go to UniProtKB: A0A3L9I213
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3L9I213
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	249	Escherichia coli	Mutation(s): 0 Gene Names: potC, potC_1, ydcV_1, ydcV_2, ydcV_3, A5U30_002795, A6592_15955, A8499_002947, A8502_000627, A9X72_15255... potC, potC_1, ydcV_1, ydcV_2, ydcV_3, A5U30_002795, A6592_15955, A8499_002947, A8502_000627, A9X72_15255, AC065_02240, ACN81_08955, ACU57_04400, AM464_23655, APX88_13960, AW118_12280, AWP47_13345, B6R12_000504, B6R15_001757, B6R17_004874, B6R31_003316, B6R48_003778, B6R87_003691, BANRA_01659, BB540_14945, BER14_10380, BG944_003572, BGM66_002096, BHS81_07005, BJI68_20815, BJJ90_15600, BK292_02680, BK383_03465, BKL28_002184, BMT50_26175, BMT91_12665, BR158_001801, BTB68_003120, BTQ06_08260, BUO55_004571, BvCmsKKP061_02954, BvCmsSIP010_04198, BXT93_13675, BZL69_25605, C0P57_004319, C1Q91_003202, C2121_002292, C2M16_24840, C2R31_002383, C3F40_06350, C9E67_18010, C9Z68_07505, CCS08_25890, CCU84_001209, CDL36_24675, CF22_003052, CG692_05800, CG704_04285, CG831_001507, CIG67_22120, CQB02_10350, CR538_15455, CR539_10315, CR628_002750, CRM83_08715, CTR35_002409, CV83915_00460, CWS33_18945, CX938_002470, CY655_06775, D1912_28130, D3C88_20205, D3G36_11685, D4M65_04975, D4N09_21675, D6T60_02655, D9D43_24810, D9E34_12200, D9E49_04970, D9H94_04140, D9J03_17690, D9J61_03865, DD762_03445, DIV22_29215, DNQ45_21635, DNX30_11960, DS732_10685, DTL43_16090, DTL90_00550, DTM45_18130, E0I52_23200, E5H86_12355, E6D34_10760, EA239_00295, EAI46_30040, EB534_RS22165, EC95NR1_05521, ECs1500, EIA08_03100, EIZ93_12975, EN85_002805, EPS97_06545, ERS085406_04756, ERS139208_03584, EWK56_20235, ExPECSC038_03525, F7F11_10145, F7N46_02625, F9413_19575, F9461_13420, F9B07_16725, FA868_17035, FEJ01_12390, FGG80_05290, FHD44_11240, FHQ97_21900, FIJ20_07135, FJQ40_01115, FKO60_09525, FN993_001406, FOI11_007325, FOI11_14295, FPI65_06715, FPS11_22520, FTV92_08150, FV293_24155, FVB16_27920, FWK02_08455, FZN31_14455, FZU14_20790, G3V95_08225, G4A38_16225, G4A47_15585, G5603_00425, G9448_04955, GAI89_13105, GAJ12_13755, GAJ26_15290, GGB84_000449, GIB53_10960, GJ11_06755, GKF52_06310, GKF66_05355, GKF89_00460, GNW61_10815, GOP14_002872, GOP25_17230, GP711_16650, GP975_14170, GQA06_13340, GQM04_12265, GQM13_14165, GQM17_13975, GQM21_19785, GQN34_10420, GQW07_08705, GRO95_22425, GRW05_02585, GRW24_14635, GRW56_11570, GRW56_16825, GRW57_26905, GSM54_00955, GUC01_01505, GUI33_16895, H0O53_11640, H0O72_17025, H0P11_10035, H5Z35_002280, H6Y26_000713, HCQ42_003698, HEP30_012130, HEP34_001040, HHH44_002983, HI055_001520, HIE29_000017, HJQ60_002258, HJY54_000267, HKA49_003618, HLQ92_15560, HLV18_17555, HLX92_03865, HLZ50_01995, HMW38_03190, HV109_14435, HV146_09425, HV209_29260, HVV39_00230, HVW04_05415, HVW43_06265, HVY77_15600, HVZ29_08880, HVZ30_12220, HVZ71_14730, HX136_15475, I6H00_08375, I6H02_24695, IFB95_003731, IUD45_003266, J0541_003204, J4S20_003290, J5U05_002926, J7T50_002317, JFD_01769, JFD_02101, JNP96_10885, NCTC10082_00605, NCTC10089_02970, NCTC10090_00713, NCTC10418_04452, NCTC10429_05323, NCTC10487_03421, NCTC10767_05082, NCTC10865_03646, NCTC10974_03368, NCTC11126_00875, NCTC11127_00498, NCTC11181_00131, NCTC11341_04943, NCTC12950_03259, NCTC13127_04034, NCTC4450_04160, NCTC7922_00686, NCTC7927_03349, NCTC8009_05603, NCTC8333_03555, NCTC8450_03471, NCTC8500_03286, NCTC8621_03201, NCTC8622_05764, NCTC8959_00861, NCTC8960_00798, NCTC9001_00967, NCTC9045_03511, NCTC9050_05374, NCTC9071_02741, NCTC9075_03982, NCTC9077_03719, NCTC9081_03564, NCTC9111_03066, NCTC9706_00377, NCTC9775_05882, NCTC9777_03004, NEP60_22985, OS110_10890, RG28_17070, SAMEA3472044_03469, SAMEA3472056_01827, SAMEA3752557_01590, SAMEA3753106_00761, TUM18780_24840, WR15_27305 Membrane Entity: Yes
UniProt
Find proteins for C3TDI7 (Escherichia coli) Explore C3TDI7 Go to UniProtKB: C3TDI7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3TDI7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine/putrescine import ATP-binding protein PotA	D	358	Escherichia coli	Mutation(s): 1 Gene Names: potA, C2M16_24850 EC: 7.6.2.11 Membrane Entity: Yes
UniProt
Find proteins for A0A2K3TLI6 (Escherichia coli) Explore A0A2K3TLI6 Go to UniProtKB: A0A2K3TLI6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2K3TLI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPD (Subject of Investigation/LOI) Query on SPD Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth D] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth D] mmCIF format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth D]	E [auth A], F [auth A], H [auth D], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D]