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- PDB-9p00: Cryo-EM structure of apo S. Mansoni p97 -

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Basic information

Entry
Database: PDB / ID: 9p00
TitleCryo-EM structure of apo S. Mansoni p97
Componentsvesicle-fusing ATPase
KeywordsCHAPERONE / AAA-ATPase / Endoplasmic Reticulum / Hexamer
Function / homology
Function and homology information


mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / retrograde protein transport, ER to cytosol / polyubiquitin modification-dependent protein binding / autophagosome maturation / ATP hydrolysis activity / ATP binding / nucleus / cytosol
Similarity search - Function
AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / : / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily ...AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / : / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / 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
vesicle-fusing ATPase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsStephens, D.R. / Han, Y. / Chen, Z. / Collins, J.J. / Fung, H.Y.J.
Funding support United States, 5items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI167967 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150776 United States
Welch FoundationI-1948-20240404 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Leveraging the Human Druggable Genome to Uncover Therapeutic Targets in the Human Parasite Schistosoma mansoni
Authors: Stephens, D.R. / Fung, H.Y.J. / Han, Y. / Liang, J. / Chen, Z. / Ready, J. / Collins, J.J.
History
DepositionJun 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: vesicle-fusing ATPase
C: vesicle-fusing ATPase
D: vesicle-fusing ATPase
F: vesicle-fusing ATPase
B: vesicle-fusing ATPase
E: vesicle-fusing ATPase


Theoretical massNumber of molelcules
Total (without water)556,5346
Polymers556,5346
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
vesicle-fusing ATPase


Mass: 92755.594 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: First 37 residues are expression tags. / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G4M0P7, vesicle-fusing ATPase
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: Homohexamer of p97 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Schistosoma mansoni (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.4
Details: 20mM Tris (pH 7.4), 180mM NaCl, 5mM MgCl2, and 1mM tris(2-carboxyethyl)phosphine (TCEP)
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 2200 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
9ISOLDEmodel fitting
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
15MOLREPmodel refinement
16PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1949076 / Details: Template picking with CB-5083-bound map
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 478635
Details: Homogenous refinement with global CTF refinement. The map was also sharpened by deepEMhancer to obtain final map used for modeling.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: Single chain ModelAngelo model built in PDB 9OX9 was docked into this map, and undergone manual modeling in Coot. The rest of the chains were built using molrep in CCP-EM and refined.
Atomic model buildingPDB-ID: 9OX9

9ox9


Pdb chain-ID: D / Accession code: 9OX9 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.72 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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