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- EMDB-20318: Msp1-substrate complex in closed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-20318
TitleMsp1-substrate complex in closed conformation
Map dataprimary map
Sample
  • Complex: Msp1-substrate complex in closed conformation
    • Protein or peptide: Membrane-spanning ATPase-like protein
    • Protein or peptide: Unknown peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
Keywordsmembrane protein / tail-anchored protein / protein quality control / PROTEIN TRANSPORT
Function / homology
Function and homology information


extraction of mislocalized protein from mitochondrial outer membrane / mitochondrial outer membrane / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Membrane-spanning ATPase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang L / Myasnikov A
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)S10OD021741 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD020054 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.
History
DepositionJun 19, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseFeb 12, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pdw
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20318.png

Downloads & links

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Map

FileDownload / File: emd_20318.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
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 EMDB: 0.28 / Movie #1: 0.35
Minimum - Maximum-2.0836024 - 4.5090528
Average (Standard dev.)0.0053294 (±0.07552055)
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-2.0844.5090.005

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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
Components
  • Complex: Msp1-substrate complex in closed conformation
    • Protein or peptide: Membrane-spanning ATPase-like protein
    • Protein or peptide: Unknown peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Msp1-substrate complex in closed conformation

SupramoleculeName: Msp1-substrate complex in closed conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Membrane-spanning ATPase-like protein

MacromoleculeName: Membrane-spanning ATPase-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 42.599152 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSIAPYLVKI IDPDYEKNER TRIKAQENLR RIRRKQIAEK GDNEDGTDDP SRRRKIDDLV LNEYENQVAL EVVAPEDIPV GFNDIGGLD DIIEELKETI IYPLTMPHLY KHGGALLAAP SGVLLYGPPG CGKTMLAKAV AHESGASFIN LHISTLTEKW Y GDSNKIVR ...String:
GSIAPYLVKI IDPDYEKNER TRIKAQENLR RIRRKQIAEK GDNEDGTDDP SRRRKIDDLV LNEYENQVAL EVVAPEDIPV GFNDIGGLD DIIEELKETI IYPLTMPHLY KHGGALLAAP SGVLLYGPPG CGKTMLAKAV AHESGASFIN LHISTLTEKW Y GDSNKIVR AVFSLAKKLQ PSIIFIDEID AVLGTRRSGE HEASGMVKAE FMTLWDGLTS TNASGVPNRI VVLGATNRIN DI DEAILRR MPKQFPVPLP GLEQRRRILE LVLRGTKRDP DFDLDYIARV TAGMSGSDIK ETCRDAAMAP MREYIRQHRA SGK PLSEIN PDDVRGIRTE DFFGRRGGKI LSEIPPRQTG YVVQSKNSSE GGYEEVEDDD EQGTAST

UniProtKB: Membrane-spanning ATPase-like protein

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Macromolecule #2: Unknown peptide

MacromoleculeName: Unknown peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 869.063 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / 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

Concentration4 mg/mL
BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48861
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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