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- EMDB-45192: Cryo-EM structure of PqqU with ligand PQQ -

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Basic information

Entry
Database: EMDB / ID: EMD-45192
TitleCryo-EM structure of PqqU with ligand PQQ
Map dataCryo-EM structure of E. coli PqqU with ligand PQQ at 1.99 A global resolution.
Sample
  • Complex: Complex of PqqU with PQQ
    • Protein or peptide: Pyrroloquinoline quinone transporter
  • Ligand: CALCIUM ION
  • Ligand: PYRROLOQUINOLINE QUINONE
  • Ligand: water
KeywordsTonD-dependent / outer membrane / transporter / PQQ uptake / MEMBRANE PROTEIN
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / intracellular monoatomic cation homeostasis / transmembrane transporter complex / cell outer membrane / signaling receptor activity / membrane
Similarity search - Function
: / TonB-dependent siderophore receptor / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
Pyrroloquinoline quinone transporter
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsMunder F / Venugopal H / Grinter R
Funding support Australia, 4 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1197376 Australia
Australian Research Council (ARC)DP230102150 Australia
Australian Research Council (ARC)LE200100045 Australia
Australian Research Council (ARC)LE120100090 Australia
CitationJournal: Sci Adv / Year: 2025
Title: High-affinity PQQ import is widespread in Gram-negative bacteria.
Authors: Fabian Munder / Marcos Voutsinos / Klaus Hantke / Hari Venugopal / Rhys Grinter /
Abstract: Pyrroloquinoline quinone (PQQ) is a soluble redox cofactor used by diverse bacteria. Many Gram-negative bacteria that encode PQQ-dependent enzymes do not produce it and instead obtain it from the ...Pyrroloquinoline quinone (PQQ) is a soluble redox cofactor used by diverse bacteria. Many Gram-negative bacteria that encode PQQ-dependent enzymes do not produce it and instead obtain it from the environment. To achieve this, uses the TonB-dependent transporter PqqU as a high-affinity PQQ importer. Here, we show that PqqU binds PQQ with high affinity and determine the high-resolution structure of the PqqU-PQQ complex, revealing that PqqU undergoes conformational changes in PQQ binding to capture the cofactor in an internal cavity. We show that these conformational changes preclude the binding of a bacteriophage, which targets PqqU as a cell surface receptor. Guided by the PqqU-PQQ structure, we identify amino acids essential for PQQ import and leverage this information to map the presence of PqqU across Gram-negative bacteria. This reveals that PqqU is encoded by Gram-negative bacteria from at least 22 phyla occupying diverse habitats, indicating that PQQ is an important cofactor for bacteria that adopt diverse lifestyles and metabolic strategies.
History
DepositionJun 4, 2024-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45192.png

Downloads & links

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Map

FileDownload / File: emd_45192.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of E. coli PqqU with ligand PQQ at 1.99 A global resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.486
Minimum - Maximum-2.0140204 - 3.8083582
Average (Standard dev.)0.00039150973 (±0.0641263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B of PqqU with ligand PQQ.

Fileemd_45192_half_map_1.map
AnnotationHalf Map B of PqqU with ligand PQQ.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A of PqqU with ligand PQQ.

Fileemd_45192_half_map_2.map
AnnotationHalf Map A of PqqU with ligand PQQ.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of PqqU with PQQ

EntireName: Complex of PqqU with PQQ
Components
  • Complex: Complex of PqqU with PQQ
    • Protein or peptide: Pyrroloquinoline quinone transporter
  • Ligand: CALCIUM ION
  • Ligand: PYRROLOQUINOLINE QUINONE
  • Ligand: water

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Supramolecule #1: Complex of PqqU with PQQ

SupramoleculeName: Complex of PqqU with PQQ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: TonB-dependent outer membrane transporter PqqU in complex with its substrate PQQ.
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 78 KDa

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Macromolecule #1: Pyrroloquinoline quinone transporter

MacromoleculeName: Pyrroloquinoline quinone transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 78.401164 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNHHHHHHH HHHENLYFQG AMDIGINSDP ADEQTMIVSA APQVVSELDT PAAVSVVDGE EMRLATPRIN LSESLTGVPG LQVQNRQNY AQDLQLSIRG FGSRSTYGIR GIRLYVDGIP ATMPDGQGQT SNIDLSSVQN VEVLRGPFSA LYGNASGGVM N VTTQTGQQ ...String:
MSNHHHHHHH HHHENLYFQG AMDIGINSDP ADEQTMIVSA APQVVSELDT PAAVSVVDGE EMRLATPRIN LSESLTGVPG LQVQNRQNY AQDLQLSIRG FGSRSTYGIR GIRLYVDGIP ATMPDGQGQT SNIDLSSVQN VEVLRGPFSA LYGNASGGVM N VTTQTGQQ PPTIEASSYY GSFGSWRYGL KATGATGDGT QPGDVDYTVS TTRFTTHGYR DHSGAQKNLA NAKLGVRIDE AS KLSLIFN SVDIKADDPG GLTKAEWKAN PQQAPRAEQY DTRKTIKQTQ AGLRYERSLS SRDDMSVMMY AGERETTQYQ SIP MAPQLN PSHAGGVITL QRHYQGIDSR WTHRGELGVP VTFTTGLNYE NMSENRKGYN NFRLNSGMPE YGQKGELRRD ERNL MWNID PYLQTQWQLS EKLSLDAGVR YSSVWFDSND HYVTPGNGDD SGDASYHKWL PAGSLKYAMT DAWNIYLAAG RGFET PTIN ELSYRADGQS GMNLGLKPST NDTIEIGSKT RIGDGLLSLA LFQTDTDDEI VVDSSSGGRT TYKNAGKTRR QGAELA WDQ RFAGDFRVNA SWTWLDATYR SNVCNEQDCN GNRMPGIARN MGFASIGYVP EDGWYAGTEA RYMGDIMADD ENTAKAP SY TLVGLFTGYK YNYHNLTVDL FGRVDNLFDK EYVGSVIVNE SNGRYYEPSP GRNYGVGMNI AWRFE

UniProtKB: Pyrroloquinoline quinone transporter

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: PYRROLOQUINOLINE QUINONE

MacromoleculeName: PYRROLOQUINOLINE QUINONE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PQQ
Molecular weightTheoretical: 330.206 Da
Chemical component information

ChemComp-PQQ:
PYRROLOQUINOLINE QUINONE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 111 / 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

Concentration3.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris-HCl
150.0 mMNaClSodium Chloride
0.025 %C47H88O22Lauryl Maltose Neopentyl Glycol

Details: LMNG was partly removed by concentration in a 100 kDa cut-off concentrator.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3 microliters of sample.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 8744 / Average exposure time: 5.22 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2110000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v41

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 872884
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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