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- EMDB-14843: cryo-EM structure of CGT ABC transporter in nanodisc apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-14843
Titlecryo-EM structure of CGT ABC transporter in nanodisc apo state
Map data
Sample
  • Complex: CGT ABC transporter in apo form
    • Protein or peptide: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
Keywordscyclic-beta-glucan / ABC transporter / CGT / Brucella / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


ABC-type beta-glucan transporter / ABC-type beta-glucan transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Glucan exporter ATP-binding protein, NdvA / Beta-(1-->2)glucan export ATP-binding/permease protein ndvA family 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 ...Glucan exporter ATP-binding protein, NdvA / Beta-(1-->2)glucan export ATP-binding/permease protein ndvA family 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
Beta-(1-->2)glucan export ATP-binding/permease protein NdvA
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJaroslaw S / Dong CN / Frank L / Na W / Renato Z / Seunho J / Henning S / Christoph D
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_201273 Switzerland
Swiss National Science Foundation180541 Switzerland
Swiss National Science Foundation185544 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Mechanism of cyclic β-glucan export by ABC transporter Cgt of Brucella.
Authors: Jaroslaw Sedzicki / Dongchun Ni / Frank Lehmann / Na Wu / Renato Zenobi / Seunho Jung / Henning Stahlberg / Christoph Dehio /
Abstract: Polysaccharides play critical roles in bacteria, including the formation of protective capsules and biofilms and establishing specific host cell interactions. Their transport across membranes is ...Polysaccharides play critical roles in bacteria, including the formation of protective capsules and biofilms and establishing specific host cell interactions. Their transport across membranes is often mediated by ATP-binding cassette (ABC) transporters, which utilize ATP to translocate diverse molecules. Cyclic β-glucans (CβGs) are critical for host interaction of the Rhizobiales, including the zoonotic pathogen Brucella. CβGs are exported into the periplasmic space by the cyclic glucan transporter (Cgt). The interaction of an ABC transporter with a polysaccharide substrate has not been visualized so far. Here we use single-particle cryoelectron microscopy to elucidate the structures of Cgt from Brucella abortus in four conformational states. The substrate-bound structure reveals an unusual binding pocket at the height of the cytoplasmic leaflet, whereas ADP-vanadate models hint at an alternative mechanism of substrate release. Our work provides insights into the translocation of large, heterogeneous substrates and sheds light on protein-polysaccharide interactions in general.
History
DepositionApr 24, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14843.png

Downloads & links

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Map

FileDownload / File: emd_14843.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 240 pix.
= 246. Å		1.03 Å/pix.
x 240 pix.
= 246. Å		1.03 Å/pix.
x 240 pix.
= 246. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-3.7213235 - 5.966624
Average (Standard dev.)0.0035766799 (±0.119874135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_14843_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_14843_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14843_half_map_2.map
Projections & Slices
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Sample components

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Entire : CGT ABC transporter in apo form

EntireName: CGT ABC transporter in apo form
Components
  • Complex: CGT ABC transporter in apo form
    • Protein or peptide: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

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Supramolecule #1: CGT ABC transporter in apo form

SupramoleculeName: CGT ABC transporter in apo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Brucella abortus 2308 (bacteria)
Molecular weightTheoretical: 125 KDa

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Macromolecule #1: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA

MacromoleculeName: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type beta-glucan transporter
Source (natural)Organism: Brucella abortus 2308 (bacteria) / Strain: 2308
Molecular weightTheoretical: 66.027914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLLKIYWRA MQYLAVERTA TITMCVASVL VALVTLAEPV LFGRVIQSIS DKGDIFSPLL MWAALGGFNI MAAVFVARGA DRLAHRRRL GVMIDSYERL ITMPLAWHQK RGTSNALHTL IRATDSLFTL WLEFMRQHLT TVVALATLIP VAMTMDMRMS L VLIVLGVI ...String:
MSLLKIYWRA MQYLAVERTA TITMCVASVL VALVTLAEPV LFGRVIQSIS DKGDIFSPLL MWAALGGFNI MAAVFVARGA DRLAHRRRL GVMIDSYERL ITMPLAWHQK RGTSNALHTL IRATDSLFTL WLEFMRQHLT TVVALATLIP VAMTMDMRMS L VLIVLGVI YVMIGQLVMR KTKDGQAAVE KHHHKLFEHV SDTISNVSVV QSYNRIASET QALRDYAKNL ENAQFPVLNW WA LASGLNR MASTFSMVVV LVLGAYFVTK GQMRVGDVIA FIGFAQLMIG RLDQISAFIN QTVTARAKLE EFFQMEDATA DRQ EPENVA DLNDVKGDIV FDNVTYEFPN SGQGVYDVSF EVKPGQTVAI VGPTGAGKTT LINLLQRVFD PAAGRIMIDG TDTR TVSRR SLRHAIATVF QDAGLFNRSV EDNIRVGRAN ATHEEVHAAA KAAAAHDFIL AKSEGYDTFV GERGSQLSGG ERQRL AIAR AILKDSPILV LDEATSALDV ETEEKVTQAV DELSHNRTTF IIAHRLSTVR SADLVLFMDK GHLVESGSFN ELAERG GRF SDLLRAGGLK LEDKQPKQPV VEGSNVMPFP VKGAVA

UniProtKB: Beta-(1-->2)glucan export ATP-binding/permease protein NdvA

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Macromolecule #2: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Detailsabc transporter

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
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: 575806
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 383591
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 180
Output model

PDB-7zo8:
cryo-EM structure of CGT ABC transporter in nanodisc apo state

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