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- EMDB-53123: Nucleotide-free wild type Wzm-Wzt from Mycobacterium abscessus in LMNG -

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Basic information

Entry
Database: EMDB / ID: EMD-53123
TitleNucleotide-free wild type Wzm-Wzt from Mycobacterium abscessus in LMNG
Map dataCryo-EM map of the nucleotide-free wild type Wzm-Wzt from Mycobacterium abscessus in LMNG at 3.5 A resolution. Map was sharpened with a b factor of 95 A2
Sample
  • Complex: Wzm-Wzt
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: Lauryl Maltose Neopentyl Glycol
KeywordsABC transporter Type V ABC transporter Arabinogalactan precursor Lipid-linked galactan exporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


teichoic-acid-transporting ATPase / lipopolysaccharide transport / 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 / Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 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 12, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53123.png

Downloads & links

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Map

FileDownload / File: emd_53123.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the nucleotide-free wild type Wzm-Wzt from Mycobacterium abscessus in LMNG at 3.5 A resolution. Map was sharpened with a b factor of 95 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: 0.297
Minimum - Maximum-1.1601212 - 1.7834358
Average (Standard dev.)0.0016476897 (±0.038724173)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_53123_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_53123_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)

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

Fileemd_53123_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)

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Sample components

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Entire : Wzm-Wzt

EntireName: Wzm-Wzt
Components
  • Complex: Wzm-Wzt
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
    • Protein or peptide: ABC transporter ATP-binding protein
  • Ligand: Lauryl Maltose Neopentyl Glycol

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Supramolecule #1: Wzm-Wzt

SupramoleculeName: Wzm-Wzt / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacteroides abscessus (bacteria)

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Macromolecule #1: Probable O-antigen/lipopolysaccharide transport integral membrane...

MacromoleculeName: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
type: protein_or_peptide / ID: 1 / Details: MGSSHHHHHHSQ - expression tag (AV0) - LMNG / 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: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD

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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: 28.76401 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 EDAHDG

UniProtKB: ABC transporter ATP-binding protein

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Macromolecule #3: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 3 / Number of copies: 2 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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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

Concentration2 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl pH 8.0, 300 mM NaCl, 0.002% LMNG
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: 15mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: 1563 / Average exposure time: 1.3 sec. / Average electron dose: 63.36 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

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Image processing

Particle selectionNumber selected: 850871
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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35628
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9qfx:
Nucleotide-free wild type Wzm-Wzt from Mycobacterium abscessus in LMNG

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