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- EMDB-8527: MalFGK2 ADP-ALF4 -

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Basic information

Entry
Database: EMDB / ID: EMD-8527
TitleMalFGK2 ADP-ALF4
Map dataMalFGK2 ADP-ALF4
Sample
  • Complex: MalFGK2 ADP-AlF4
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: 23.3 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 MalK2 and Catalytic Roles of ATP, MalE, and Maltose.
Authors: Fabre L / Bao H / Innes J / Duong F / Rouiller I
History
DepositionDec 21, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseMar 1, 2017-
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: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol

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Map

FileDownload / File: emd_8527.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMalFGK2 ADP-ALF4
Voxel sizeX=Y=Z: 2.23 Å
Density
Contour LevelBy AUTHOR: 0.0209 / Movie #1: 0.02
Minimum - Maximum-0.039551314 - 0.06315778
Average (Standard dev.)0.00019759948 (±0.0054786126)
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-0.0400.0630.000

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Supplemental data

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Sample components

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Entire : MalFGK2 ADP-AlF4

EntireName: MalFGK2 ADP-AlF4
Components
  • Complex: MalFGK2 ADP-AlF4

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Supramolecule #1: MalFGK2 ADP-AlF4

SupramoleculeName: MalFGK2 ADP-AlF4 / type: complex / ID: 1 / Parent: 0
Details: Maltose Transporter MalFGK2 in complex with ADP-AlF4
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant plasmid: pBAD22-FGK

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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
1.0 mMADP
1.0 mMAlF4
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-AlF4.

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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: 9249
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: 23.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 6382
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION

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