[English] 日本語
Yorodumi
- EMDB-43498: Mechanistic Insights Revealed by YbtPQ in the Occluded State -

+
Open data


ID or keywords:

Loading...

-
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


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / 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-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43498.png

Downloads & links

-
Map

FileDownload / File: emd_43498.map.gz / Format: CCP4 / Size: 5.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
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 °

-
Supplemental data

-
Half map: #1

Fileemd_43498_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43498_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
Supramolecule #1: YbtPQ

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

-
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

-
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

-
Macromolecule #3: MAGNESIUM ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more