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- EMDB-62428: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) i... -

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Basic information

Entry
Database: EMDB / ID: EMD-62428
TitleNanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
Map data
Sample
  • Complex: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
    • Protein or peptide: Outer mitochondrial transmembrane helix translocase
    • Protein or peptide: An unknown peptide substrate
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsComplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / extraction of mislocalized protein from mitochondrial outer membrane / membrane protein dislocase activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / protein hexamerization / peroxisomal membrane / protein targeting to mitochondrion / mitochondrial outer membrane / ATP hydrolysis activity / mitochondrion / 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
Outer mitochondrial transmembrane helix translocase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsChengdong H / Simin W / Xuan C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
Authors: Chengdong H / Simin W / Xuan C
History
DepositionNov 15, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62428.png

Downloads & links

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Map

FileDownload / File: emd_62428.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.41 Å/pix.
x 540 pix.
= 221.4 Å		0.41 Å/pix.
x 540 pix.
= 221.4 Å		0.41 Å/pix.
x 540 pix.
= 221.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.41 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.18670501 - 0.29533646
Average (Standard dev.)0.00013599147 (±0.010632569)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 221.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62428_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62428_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) i...

EntireName: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
Components
  • Complex: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
    • Protein or peptide: Outer mitochondrial transmembrane helix translocase
    • Protein or peptide: An unknown peptide substrate
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) i...

SupramoleculeName: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Outer mitochondrial transmembrane helix translocase

MacromoleculeName: Outer mitochondrial transmembrane helix translocase / type: protein_or_peptide / ID: 1 / Details: Haved deleted residues 1-32 of Msp1. / Number of copies: 9 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 36.787133 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: DVESGPLSGK SRESKAKQSL QWEKLVKRSP ALAEVTLDAY ERTILSSIVT PDEINITFQD IGGLDPLISD LHESVIYPLM MPEVYSNSP LLQAPSGVLL YGPPGCGKTM LAKALAKESG ANFISIRMSS IMDKWYGESN KIVDAMFSLA NKLQPCIIFI D QIDSFLRE ...String:
DVESGPLSGK SRESKAKQSL QWEKLVKRSP ALAEVTLDAY ERTILSSIVT PDEINITFQD IGGLDPLISD LHESVIYPLM MPEVYSNSP LLQAPSGVLL YGPPGCGKTM LAKALAKESG ANFISIRMSS IMDKWYGESN KIVDAMFSLA NKLQPCIIFI D QIDSFLRE RSSTDHEVTA TLKAEFMTLW DGLLNNGRVM IIGATNRIND IDDAFLRRLP KRFLVSLPGS DQRYKILSVL LK DTKLDED EFDLQLIADN TKGFSGSDLK ELCREAALDA AKEYIKQKRQ LIDSGTIDVN DTSSLKIRPL KTKDFTKKLR MDA TSTLSS QPLD

UniProtKB: Outer mitochondrial transmembrane helix translocase

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Macromolecule #2: An unknown peptide substrate

MacromoleculeName: An unknown peptide substrate / type: protein_or_peptide / ID: 2 / Details: The sequence of this peptide substrate is unknown. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 1.720111 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 9 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 9 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 158491
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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