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- EMDB-10549: The structure of ABC transporter Rv1819c without addition of substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-10549
TitleThe structure of ABC transporter Rv1819c without addition of substrate
Map data
Sample
  • Complex: dimer of Rv1819c
    • Protein or peptide: ABC transporter ATP-binding protein/permease
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordscobalamin / vitamin B12 / ABC transporter / exporter fold / import / tuberculosis / TRANSPORT PROTEIN
Function / homology
Function and homology information


response to host immune response / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type transporter activity / ATP hydrolysis activity / extracellular region / ATP binding / membrane / plasma membrane
Similarity search - Function
ABC transporter transmembrane region 2 / : / 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. ...ABC transporter transmembrane region 2 / : / 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
Drug-transport transmembrane ATP-binding protein ABC transporter BacA / Hydrophilic compounds import ATP-binding/permease protein BacA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsRempel S / Gati C
CitationJournal: Nature / Year: 2020
Title: A mycobacterial ABC transporter mediates the uptake of hydrophilic compounds.
Authors: S Rempel / C Gati / M Nijland / C Thangaratnarajah / A Karyolaimos / J W de Gier / A Guskov / D J Slotboom /
Abstract: Mycobacterium tuberculosis (Mtb) is an obligate human pathogen and the causative agent of tuberculosis. Although Mtb can synthesize vitamin B (cobalamin) de novo, uptake of cobalamin has been linked ...Mycobacterium tuberculosis (Mtb) is an obligate human pathogen and the causative agent of tuberculosis. Although Mtb can synthesize vitamin B (cobalamin) de novo, uptake of cobalamin has been linked to pathogenesis of tuberculosis. Mtb does not encode any characterized cobalamin transporter; however, the gene rv1819c was found to be essential for uptake of cobalamin. This result is difficult to reconcile with the original annotation of Rv1819c as a protein implicated in the transport of antimicrobial peptides such as bleomycin. In addition, uptake of cobalamin seems inconsistent with the amino acid sequence, which suggests that Rv1819c has a bacterial ATP-binding cassette (ABC)-exporter fold. Here, we present structures of Rv1819c, which reveal that the protein indeed contains the ABC-exporter fold, as well as a large water-filled cavity of about 7,700 Å, which enables the protein to transport the unrelated hydrophilic compounds bleomycin and cobalamin. On the basis of these structures, we propose that Rv1819c is a multi-solute transporter for hydrophilic molecules, analogous to the multidrug exporters of the ABC transporter family, which pump out structurally diverse hydrophobic compounds from cells.
History
DepositionDec 16, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseApr 1, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tqe
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10549.png

Downloads & links

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Map

FileDownload / File: emd_10549.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 280 pix.
= 238.588 Å		0.85 Å/pix.
x 280 pix.
= 238.588 Å		0.85 Å/pix.
x 280 pix.
= 238.588 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8521 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-11.70424 - 20.455832999999998
Average (Standard dev.)-0.000000000007103 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.588 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85210.85210.8521
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z238.588238.588238.588
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-11.70420.456-0.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_10549_additional.map
Annotationunsharpened 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 : dimer of Rv1819c

EntireName: dimer of Rv1819c
Components
  • Complex: dimer of Rv1819c
    • Protein or peptide: ABC transporter ATP-binding protein/permease
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: dimer of Rv1819c

SupramoleculeName: dimer of Rv1819c / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: ABC transporter ATP-binding protein/permease

MacromoleculeName: ABC transporter ATP-binding protein/permease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 72.422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGPKLFKPSI DWSRAFPDSV YWVGKAWTIS AICVLAILVL LRYLTPWGRQ FWRITRAYFV GPNSVRVWLM LGVLLLSVVL AVRLNVLFS YQGNDMYTAL QKAFEGIASG DGTVKRSGVR GFWMSIGVFS VMAVLHVTRV MADIYLTQRF IIAWRVWLTH H LTQDWLDG ...String:
MGPKLFKPSI DWSRAFPDSV YWVGKAWTIS AICVLAILVL LRYLTPWGRQ FWRITRAYFV GPNSVRVWLM LGVLLLSVVL AVRLNVLFS YQGNDMYTAL QKAFEGIASG DGTVKRSGVR GFWMSIGVFS VMAVLHVTRV MADIYLTQRF IIAWRVWLTH H LTQDWLDG RAYYRDLFID ETIDNPDQRI QQDVDIFTAG AGGTPNAPSN GTASTLLFGA VQSIISVISF TAILWNLSGT LN IFGVSIP RAMFWTVLVY VFVATVISFI IGRPLIWLSF RNEKLNAAFR YALVRLRDAA EAVGFYRGER VEGTQLQRRF TPV IDNYRR YVRRSIAFNG WNLSVSQTIV PLPWVIQAPR LFAGQIDFGD VGQTATSFGN IHDSLSFFRN NYDAFASFRA AIIR LHGLV DANEKGRALP AVLTRPSDDE SVELNDIEVR TPAGDRLIDP LDVRLDRGGS LVITGRSGAG KTTLLRSLAE LWPYA SGTL HRPGGENETM FLSQLPYVPL GTLRDVVCYP NSAAAIPDAT LRDTLTKVAL APLCDRLDEE RDWAKVLSPG EQQRVA FAR ILLTKPKAVF LDGSTSALDT GLEFALYQLL RSELPDCIVI SVSHRPALER LHENQLELLG GGQWRLAPVE AAPAEVH HH HHHHH

UniProtKB: Drug-transport transmembrane ATP-binding protein ABC transporter BacA

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / 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 #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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35890
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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