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- EMDB-80144: Mtb galactan transporter Rv3781/3783, ATP-bound -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-80144
TitleMtb galactan transporter Rv3781/3783, ATP-bound
Map data
Sample
  • Complex: Galactan Transporter Complex
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


lipopolysaccharide transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / 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
Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE / Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsWei C / Zhang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32394011 China
CitationJournal: To Be Published
Title: Rv3781/3783 complex, NBD_Closed state
Authors: Wei C / Zhang L
History
DepositionApr 6, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80144.png

Downloads & links

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Map

FileDownload / File: emd_80144.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-5.049254 - 8.180584
Average (Standard dev.)-0.0025725937 (±0.0987472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_80144_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80144_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 : Galactan Transporter Complex

EntireName: Galactan Transporter Complex
Components
  • Complex: Galactan Transporter Complex
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
    • Protein or peptide: Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Galactan Transporter Complex

SupramoleculeName: Galactan Transporter Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 125 KDa

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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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 32.369197 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTFMDAQASF QTQSRTLARV RGDLVDGFRR HELWLHLGWQ DIKQRYRRSV LGPFWITIAT GTTAVAMGGL YSKLFRLELS EHLPYVTLG LIVWNLINAA ILDGAEVFVA NEGLIKQLPA PLSVHVYRLV WRQMIFFAHN IVIYFVIAII FPKPWSWADL S FLPALALI ...String:
MTFMDAQASF QTQSRTLARV RGDLVDGFRR HELWLHLGWQ DIKQRYRRSV LGPFWITIAT GTTAVAMGGL YSKLFRLELS EHLPYVTLG LIVWNLINAA ILDGAEVFVA NEGLIKQLPA PLSVHVYRLV WRQMIFFAHN IVIYFVIAII FPKPWSWADL S FLPALALI FLNCVWVSLC FGILATRYRD IGPLLFSVVQ LLFFMTPIIW NDETLRRQGA GRWSSIVELN PLLHYLDIVR AP LLGAHQE LRHWLVVLVL TVVGWMLAAF AMRQYRARVP YWV

UniProtKB: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD

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Macromolecule #2: Probable O-antigen/lipopolysaccharide transport ATP-binding prote...

MacromoleculeName: Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 29.998326 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: VSDPHHPHIQ THNAWVEFPI FDAKSRSLKK AVLGKAGGTI GRNNSNVVVI EALRDITMEL NLGDRVGLVG HNGAGKSTLL RLLSGIYEP TRGWAKVTGR VAPVFDLGIG MDPEISGYEN IIIRGLFLGQ TRKQMQAKVD EIAEFTELGE YLSMPLRTYS T GMRVRLAM ...String:
VSDPHHPHIQ THNAWVEFPI FDAKSRSLKK AVLGKAGGTI GRNNSNVVVI EALRDITMEL NLGDRVGLVG HNGAGKSTLL RLLSGIYEP TRGWAKVTGR VAPVFDLGIG MDPEISGYEN IIIRGLFLGQ TRKQMQAKVD EIAEFTELGE YLSMPLRTYS T GMRVRLAM GVVTSIDPEI LLLDQGIGAV DADFLRKAQS RLQNLVERSG ILVFASHSNE FLARLCKTAI WIDHGVIRLA GG IEEVVRA YEGEDAARHV REVLAETQAD RQNVQG

UniProtKB: Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE

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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: 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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / 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

Concentration10 mg/mL
BufferpH: 7.5 / Details: 150mM NaCl, 50mM Hepes
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum
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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 391925
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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