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- EMDB-43498: Mechanistic Insights Revealed by YbtPQ in the Occluded State -

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Basic information

Entry
Database: EMDB / ID: EMD-43498
TitleMechanistic Insights Revealed by YbtPQ in the Occluded State
Map data
Sample
  • Complex: YbtPQ
    • Protein or peptide: ABC transporter ATP-binding protein
    • Protein or peptide: Permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ
  • Ligand: MAGNESIUM ION
  • Ligand: ADP ORTHOVANADATE
KeywordsABC importer / siderophore / occluded / MEMBRANE PROTEIN
Function / homology
Function and homology information


oligopeptide export from mitochondrion / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ABC-type oligopeptide transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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
ABC transporter ATP-binding protein / Permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHu W / Parkinson C / Zheng H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI175646 United States
CitationJournal: Biomolecules / Year: 2024
Title: Mechanistic Insights Revealed by YbtPQ in the Occluded State.
Authors: Wenxin Hu / Chance Parkinson / Hongjin Zheng /
Abstract: Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of ...Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of "alternating access" like those exporters, cycling through inward-open, occluded, and outward-open conformations. Understanding how the exporter-like importers move substrates in the opposite direction requires structural studies on all the major conformations. To shed light on this, here we report the structure of yersiniabactin importer YbtPQ from uropathogenic in the occluded conformation trapped by ADP-vanadate (ADP-Vi) at a 3.1 Å resolution determined by cryo-electron microscopy. The structure shows unusual local rearrangements in multiple helices and loops in its transmembrane domains (TMDs). In addition, the dimerization of the nucleotide-binding domains (NBDs) promoted by the vanadate trapping is highlighted by the "screwdriver" action at one of the two hinge points. These structural observations are rare and thus provide valuable information to understand the structural plasticity of the exporter-like ABC importers.
History
DepositionJan 24, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43498.png

Downloads & links

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Map

FileDownload / File: emd_43498.map.gz / Format: CCP4 / Size: 5.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 87 pix.
= 72.21 Å		0.83 Å/pix.
x 102 pix.
= 84.66 Å		0.83 Å/pix.
x 161 pix.
= 133.63 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.86
Minimum - Maximum-2.3799148 - 5.07191
Average (Standard dev.)-0.000000000006479 (±0.37703192)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin10871120
Dimensions10216187
Spacing87102161
CellA: 72.21 Å / B: 84.659996 Å / C: 133.63 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43498_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43498_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : YbtPQ

EntireName: YbtPQ
Components
  • Complex: YbtPQ
    • Protein or peptide: ABC transporter ATP-binding protein
    • Protein or peptide: Permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ
  • Ligand: MAGNESIUM ION
  • Ligand: ADP ORTHOVANADATE

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Supramolecule #1: YbtPQ

SupramoleculeName: YbtPQ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: ABC transporter ATP-binding protein

MacromoleculeName: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 66.348664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSQSSNTES LSRFPLWQVI TPVRRKVILA MALAGLAALT SLGALLFLAW SLRDIRATPD AIPAWPLGGV IGCVVLTFVL RLQAFNTSH YAAFHLENIL RSRLARKALQ LPPGVLQQMG SGSVAKVMLD DVKSLHIFVA DSTPLYARAI IMPLATIVIL F WLDWRLAI ...String:
MSSQSSNTES LSRFPLWQVI TPVRRKVILA MALAGLAALT SLGALLFLAW SLRDIRATPD AIPAWPLGGV IGCVVLTFVL RLQAFNTSH YAAFHLENIL RSRLARKALQ LPPGVLQQMG SGSVAKVMLD DVKSLHIFVA DSTPLYARAI IMPLATIVIL F WLDWRLAI ATLGVLAFGS VVLVLARQRS ENMAQRYHKA REQVSAAVIE FVQAMPVVRT FDSGSTSFLR YQRALEEWVD VL KTWYRKA GFSARFSFSI LNPLPTLFVL IWSGYGLLHY GSFDFIAWVA VLLLGSGMAE AVMPMMMLNN LVAQTRLSIQ RIY QVLAMP ELSLPQSDQQ PQEASITFEQ VSFHYPQART GAALQEVSFH VPAGQIVALV GPSGAGKSTV ARLLLRYADP DKGH IRIGG VDLRDMQTDT LMKQLSFVFQ DNFLFADTIA NNIRLGAPDT PLEAVIAAAR VAQAHDFISA LPEGYNTRVG ERGVF LSGG QRQRITIARA LLQDRPILVL DEATAFADPE NEAALIKALA AAMRGRTVIM VAHRLSMVTQ ADVILLFSDG QLREMG NHT QLLAQGGLYQ RLWQHYQQAQ HWVPGGTQEE VVENERQ

UniProtKB: ABC transporter ATP-binding protein

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Macromolecule #2: Permease and ATP-binding protein of yersiniabactin-iron ABC trans...

MacromoleculeName: Permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 66.526086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDNNPADNL AWRVIWRQLI SSVGSQARML RRSMLALLLA AFMQGIAFAC LYPIIDALLR GDAPQLLNWA MAFSVAAIVT LVLRWYGLG FEYRGHLAQA THELRLRLGE QLRRVPLEKL QRGRAGEMNA LLLGSVDENL NYVIAIANIL LLTIVTPLTA S LATLWIDW ...String:
MKDNNPADNL AWRVIWRQLI SSVGSQARML RRSMLALLLA AFMQGIAFAC LYPIIDALLR GDAPQLLNWA MAFSVAAIVT LVLRWYGLG FEYRGHLAQA THELRLRLGE QLRRVPLEKL QRGRAGEMNA LLLGSVDENL NYVIAIANIL LLTIVTPLTA S LATLWIDW RLGLVMLLIF PLLVPFYYWR RPAMRRQMQT LGEAHQRLSG DIVEFAQGMM VLRTCGSDAD KSRALLAHFN AL ENLQTRT HRQGAGATML IASVVELGLQ VVVLSGIVWV VTGTLNLAFL IAAVAMIMRF AEPMAMFISY TSVVELIASA LQR IEQFMA IAPLPVAEQS EMPERYDIRF DNVSYRYEEG DGYALNHVSL TFPAASMSAL VGASGAGKTT VTKLLMRYAD PQQG QISIG GVDIRRLTPE QLNSLISVVF QDVWLFDDTL LANIRIARPQ ATRQEVEEAA RAAQCLEFIS RLPQGWLTPM GEMGG QLSG GERQRISIAR ALLKNAPVVI LDEPTAALDI ESELAVQKAI DNLVHNRTVI IIAHRLSTIA GAGNILVMEE GQVVEQ GTH AQLLSHHGRY QALWQAQMAA RVWRDDGVSA SGEWVHE

UniProtKB: Permease and ATP-binding protein of yersiniabactin-iron ABC transporter YbtQ

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADP ORTHOVANADATE

MacromoleculeName: ADP ORTHOVANADATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: AOV
Molecular weightTheoretical: 544.156 Da
Chemical component information

ChemComp-AOV:
ADP ORTHOVANADATE / energy-carrying molecule analogue*YM

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 340080
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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