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- PDB-9kmd: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) i... -

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Basic information

Entry
Database: PDB / ID: 9kmd
TitleNanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
Components
  • An unknown peptide substrate
  • Outer mitochondrial transmembrane helix translocase
KeywordsMEMBRANE PROTEIN / Complex
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
ADENOSINE-5'-TRIPHOSPHATE / Outer mitochondrial transmembrane helix translocase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsChengdong, H. / Simin, W. / Xuan, C.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer mitochondrial transmembrane helix translocase
B: Outer mitochondrial transmembrane helix translocase
C: Outer mitochondrial transmembrane helix translocase
D: Outer mitochondrial transmembrane helix translocase
E: Outer mitochondrial transmembrane helix translocase
F: Outer mitochondrial transmembrane helix translocase
G: Outer mitochondrial transmembrane helix translocase
H: Outer mitochondrial transmembrane helix translocase
I: Outer mitochondrial transmembrane helix translocase
J: An unknown peptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,58828
Polymers332,80410
Non-polymers4,78318
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Outer mitochondrial transmembrane helix translocase / Mitochondrial sorting of proteins / Tat-binding homolog 4


Mass: 36787.133 Da / Num. of mol.: 9 / Mutation: E193Q
Source method: isolated from a genetically manipulated source
Details: Haved deleted residues 1-32 of Msp1. / Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MSP1, YTA4, YGR028W / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P28737, Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
#2: Protein/peptide An unknown peptide substrate


Mass: 1720.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence of this peptide substrate is unknown. / Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nanomer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158491 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00621918
ELECTRON MICROSCOPYf_angle_d0.71229593
ELECTRON MICROSCOPYf_dihedral_angle_d6.0832923
ELECTRON MICROSCOPYf_chiral_restr0.0453389
ELECTRON MICROSCOPYf_plane_restr0.0063706

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