[English] 日本語
Yorodumi
- EMDB-53181: ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in nanodiscs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53181
TitleATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in nanodiscs
Map dataCryo-EM map of the ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in nanodiscs at 3.3 A resolution. Map was sharpened with a b factor of 132 A2
Sample
  • Complex: Wzm-Wzt
    • Protein or peptide: ABC transporter permease
  • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsABC transporter Type V ABC transporter Arabinogalactan precursor Lipid-linked galactan exporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


teichoic-acid-transporting ATPase / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ABC transporter, teichoic acids export TagH-like / : / ABC-2 type transporter / ABC-2 type transporter / 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 / ABC transporter permease
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGaraeva AA / Fabianova V / Savkova K / Huszar S / Xue X / Lowary TL / Mikusova K / Seeger MA
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)772190European Union
Swiss National Science FoundationPP00P3_170625 Switzerland
European Union (EU)NextGenerationEU, Recovery and Resilience Plan for Slovakia, project No. 09I01-03-V03- 00001European Union
University of ZurichFK-21-041 Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of lipid-linked galactan export by the mycobacterial ABC transporter Wzm-Wzt
Authors: Garaeva AA / Fabianova V / Savkova K / Huszar S / Xue X / Lowary TL / Mikusova K / Seeger MA
History
DepositionMar 16, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53181.png

Downloads & links

-
Map

FileDownload / File: emd_53181.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in nanodiscs at 3.3 A resolution. Map was sharpened with a b factor of 132 A2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.292
Minimum - Maximum-1.4155577 - 2.1535282
Average (Standard dev.)0.0007834265 (±0.049160115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53181_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map A used for post processing step and...

Fileemd_53181_half_map_1.map
Annotationhalf-map A used for post processing step and FSC resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map B used for post processing step and...

Fileemd_53181_half_map_2.map
Annotationhalf-map B used for post processing step and FSC resolution calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Wzm-Wzt

EntireName: Wzm-Wzt
Components
  • Complex: Wzm-Wzt
    • Protein or peptide: ABC transporter permease
  • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Wzm-Wzt

SupramoleculeName: Wzm-Wzt / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacteroides abscessus (bacteria)

-
Macromolecule #1: ABC transporter permease

MacromoleculeName: ABC transporter permease / type: protein_or_peptide / ID: 1 / Details: MGSSHHHHHHSQ - expression tag / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 35.249207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQMSSSAGLT SQRPGSKEND MANELIELSS DSRTFKRAWR DLSEGFEHRQ LWLQLGWQDI KQRYRRSVLG PFWITIATG STALAMGILY SQLFKLPLAE HLPYVTIGLI VWNLFNAAIL EGSDVFVANE GLIKQLPTPL SVHVYRLVWR Q LLLFAHNI ...String:
MGSSHHHHHH SQMSSSAGLT SQRPGSKEND MANELIELSS DSRTFKRAWR DLSEGFEHRQ LWLQLGWQDI KQRYRRSVLG PFWITIATG STALAMGILY SQLFKLPLAE HLPYVTIGLI VWNLFNAAIL EGSDVFVANE GLIKQLPTPL SVHVYRLVWR Q LLLFAHNI IIFLIVVAVY TPHWHFTDLS FIPALVLITL NCLWVSLVFG VLATRYRDIS PLLGSLVQLL FFMTPIIWNE NM LNQRVGK LATVVQLNPF VHFLAIIRDP LLGLDQQLHH WIIALSITVV GWIVAIVVMR QYRARVPYWV

UniProtKB: ABC transporter permease

-
Macromolecule #2: ABC transporter ATP-binding protein

MacromoleculeName: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: teichoic-acid-transporting ATPase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 28.453727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSIQTHQAW VEFPIFDAKS RSLKKAFLGK AGGAIGRNES NVVVIEALRD ITLSLKEGDR VGLVGHNGAG KSTLLRLLSG IYEPTRGSS YIKGRVAPVF DLGVGMDPEI SGYENIIIRG MFLGQTRKQM QAKVDEIADF TELGEYLSMP LRTYSTGMRV R LAMGVVTS ...String:
MVSIQTHQAW VEFPIFDAKS RSLKKAFLGK AGGAIGRNES NVVVIEALRD ITLSLKEGDR VGLVGHNGAG KSTLLRLLSG IYEPTRGSS YIKGRVAPVF DLGVGMDPEI SGYENIIIRG MFLGQTRKQM QAKVDEIADF TELGEYLSMP LRTYSTGMRV R LAMGVVTS IDPEILLLDE GIGAVDAEFM KKARIRLQQL VERSGMLVFA SHSNEFLARL CNTAMWIDHG TIKMSGGIED VV RAYEGDE AGDHVAQILA EDA

UniProtKB: ABC transporter ATP-binding protein

-
Macromolecule #3: MAGNESIUM ION

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

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl pH 7.5, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: at 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 90.0 K / Max: 105.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12029 / Average exposure time: 1.1 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 7385222
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 90928
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
Atomic model buiding 1

Initial modelPDB ID:

9qh1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-9qhw:
ATP-bound wild type Wzm-Wzt from Mycobacterium abscessus in nanodiscs

+
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