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- EMDB-8530: MalE-MalFGK2 ADP-V04 -

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Basic information

Entry
Database: EMDB / ID: EMD-8530
TitleMalE-MalFGK2 ADP-V04
Map dataMalFGK2 ADP
Sample
  • Complex: MalE-MalFGK2 ADP-VO4
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / DNA-binding transcription factor binding / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / : ...Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / : / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / 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. / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 20.5 Å
AuthorsFabre L / Bao H / Innes J / Duong F / Rouiller I
CitationJournal: J Biol Chem / Year: 2017
Title: Negative Stain Single-particle EM of the Maltose Transporter in Nanodiscs Reveals Asymmetric Closure of MalK and Catalytic Roles of ATP, MalE, and Maltose.
Authors: Lucien Fabre / Huan Bao / James Innes / Franck Duong / Isabelle Rouiller /
Abstract: The MalE-MalFGK complex is one of the best characterized members of the large and ubiquitous family of ATP-binding cassette (ABC) transporters. It is composed of a membrane-spanning heterodimer, ...The MalE-MalFGK complex is one of the best characterized members of the large and ubiquitous family of ATP-binding cassette (ABC) transporters. It is composed of a membrane-spanning heterodimer, MalF-MalG; a homodimeric ATPase, MalK; and a periplasmic maltose receptor, MalE. Opening and closure of MalK is coupled to conformational changes in MalF-MalG and the alternate exposition of the substrate-binding site to either side of the membrane. To further define this alternate access mechanism and the impact of ATP, MalE, and maltose on the conformation of the transporter during the transport cycle, we have reconstituted MalFGK in nanodiscs and analyzed its conformations under 10 different biochemical conditions using negative stain single-particle EM. EM map results (at 15-25 Å resolution) indicate that binding of ATP to MalK promotes an asymmetric, semi-closed conformation in accordance with the low ATPase activity of MalFGK In the presence of MalE, the MalK dimer becomes fully closed, gaining the ability to hydrolyze ATP. In the presence of ADP or maltose, MalE·MalFGK remains essentially in a semi-closed symmetric conformation, indicating that release of these ligands is required for the return to the initial state. Taken together, this structural information provides a rationale for the stimulation of MalK ATPase activity by MalE as well as by maltose.
History
DepositionDec 21, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseJan 24, 2018-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8530.png

Downloads & links

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Map

FileDownload / File: emd_8530.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMalFGK2 ADP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.23 Å/pix.
x 120 pix.
= 267.6 Å		2.23 Å/pix.
x 120 pix.
= 267.6 Å		2.23 Å/pix.
x 120 pix.
= 267.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0292 / Movie #1: 0.021
Minimum - Maximum-0.027450979 - 0.050781693
Average (Standard dev.)0.00062048546 (±0.005548846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 267.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.232.232.23
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z267.600267.600267.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.0270.0510.001

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Supplemental data

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Sample components

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Entire : MalE-MalFGK2 ADP-VO4

EntireName: MalE-MalFGK2 ADP-VO4
Components
  • Complex: MalE-MalFGK2 ADP-VO4

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Supramolecule #1: MalE-MalFGK2 ADP-VO4

SupramoleculeName: MalE-MalFGK2 ADP-VO4 / type: complex / ID: 1 / Parent: 0
Details: Maltose Transporter MalFGK2 in complex with MalE and ADP-VO4
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant plasmid: pBAD22

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
30.0 mMTrisHCl
100.0 mMNaCl
10.0 %Glycerol
0.08 %DDM
5.0 mMMgCl2
StainingType: NEGATIVE / Material: Uranyl Formate / Details: Freshly prepared 1.5% uranyl formate (pH 5)
GridMesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
DetailsMalFGK2 reconstituted in nanodiscs at a molar ratio MalFGK2:MSP1D1:lipid (DOPC)of 1:3:60. Incubated with ADP-VO4 and MalE.

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 134010 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4 µm / Nominal defocus min: 0.7 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13275
CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: EMDB MAP
EMDB ID:

8524


Details: MalFGK2 Apo low pass filtered at 60A
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 13275
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION

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