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- EMDB-20319: Msp1-substrate complex in open conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-20319
TitleMsp1-substrate complex in open conformation
Map data
SampleMsp1-substrate complex in closed conformation:
Membrane-spanning ATPase-like protein / Unknown E. coli peptide / (ligand) x 3
Function / homologyAAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / P-loop containing nucleoside triphosphate hydrolase / AAA ATPase, AAA+ lid domain / ATPase activity / integral component of membrane / ATP binding / Membrane-spanning ATPase-like protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang L / Myasnikov A / Pan X / Walter P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM032384 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD020054 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD021741 United States
CitationJournal: Elife / Year: 2020
Title: Structure of the AAA protein Msp1 reveals mechanism of mislocalized membrane protein extraction.
Authors: Lan Wang / Alexander Myasnikov / Xingjie Pan / Peter Walter /
Abstract: The AAA protein Msp1 extracts mislocalized tail-anchored membrane proteins and targets them for degradation, thus maintaining proper cell organization. How Msp1 selects its substrates and firmly ...The AAA protein Msp1 extracts mislocalized tail-anchored membrane proteins and targets them for degradation, thus maintaining proper cell organization. How Msp1 selects its substrates and firmly engages them during the energetically unfavorable extraction process remains a mystery. To address this question, we solved cryo-EM structures of Msp1-substrate complexes at near-atomic resolution. Akin to other AAA proteins, Msp1 forms hexameric spirals that translocate substrates through a central pore. A singular hydrophobic substrate recruitment site is exposed at the spiral's seam, which we propose positions the substrate for entry into the pore. There, a tight web of aromatic amino acids grips the substrate in a sequence-promiscuous, hydrophobic milieu. Elements at the intersubunit interfaces coordinate ATP hydrolysis with the subunits' positions in the spiral. We present a comprehensive model of Msp1's mechanism, which follows general architectural principles established for other AAA proteins yet specializes Msp1 for its unique role in membrane protein extraction.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 19, 2019-
Header (metadata) releaseFeb 5, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pdy
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20319.png

Downloads & links

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Map

FileDownload / File: emd_20319.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.4
Minimum - Maximum-1.5265005 - 2.7389593
Average (Standard dev.)0.0055111246 (±0.057647236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.104271.104271.104
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.5272.7390.006

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Supplemental data

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Sample components

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Entire Msp1-substrate complex in closed conformation

EntireName: Msp1-substrate complex in closed conformation / Number of components: 6

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Component #1: protein, Msp1-substrate complex in closed conformation

ProteinName: Msp1-substrate complex in closed conformation / Recombinant expression: No
MassExperimental: 240 kDa
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: BL21DE3

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Component #2: protein, Membrane-spanning ATPase-like protein

ProteinName: Membrane-spanning ATPase-like protein / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 42.599152 kDa
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, Unknown E. coli peptide

ProteinName: Unknown E. coli peptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.869063 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #5: ligand, BERYLLIUM TRIFLUORIDE ION

LigandName: BERYLLIUM TRIFLUORIDE ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.600705 MDa

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Component #6: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/mL / pH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 70 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: DIFFRACTION
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 29723
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

6pdy

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