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- EMDB-71066: Cryo-EM structure of S. Mansoni p97 bound to compound 804 -

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Basic information

Entry
Database: EMDB / ID: EMD-71066
TitleCryo-EM structure of S. Mansoni p97 bound to compound 804
Map dataCryo-EM structure of S. Mansoni p97 bound to compound 804
Sample
  • Complex: Hexamer of p97 conjugated to inhibitor 804
    • Protein or peptide: vesicle-fusing ATPase
  • Ligand: (2Z)-N-[2-(3-methylpyridin-2-yl)-1,3-benzoxazol-5-yl]-3-(pyridin-4-yl)prop-2-enamide
KeywordsAAA-ATPase / Endoplasmic Reticulum / Hexamer / Inhibitor / CHAPERONE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsStephens DR / Han Y / Chen Z / Liang J / Ready J / Collins JJ / Fung HYJ
Funding support United States, 5 items
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 DR / Fung HYJ / Han Y / Liang J / Chen Z / Ready J / Collins JJ
History
DepositionJun 6, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71066.png

Downloads & links

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Map

FileDownload / File: emd_71066.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of S. Mansoni p97 bound to compound 804
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 280.166 Å		0.73 Å/pix.
x 384 pix.
= 280.166 Å		0.73 Å/pix.
x 384 pix.
= 280.166 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0465
Minimum - Maximum-0.0018371938 - 1.8166869
Average (Standard dev.)0.0022839082 (±0.033858884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 280.1664 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_71066_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71066_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexamer of p97 conjugated to inhibitor 804

EntireName: Hexamer of p97 conjugated to inhibitor 804
Components
  • Complex: Hexamer of p97 conjugated to inhibitor 804
    • Protein or peptide: vesicle-fusing ATPase
  • Ligand: (2Z)-N-[2-(3-methylpyridin-2-yl)-1,3-benzoxazol-5-yl]-3-(pyridin-4-yl)prop-2-enamide

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Supramolecule #1: Hexamer of p97 conjugated to inhibitor 804

SupramoleculeName: Hexamer of p97 conjugated to inhibitor 804 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Schistosoma mansoni (invertebrata)

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Macromolecule #1: vesicle-fusing ATPase

MacromoleculeName: vesicle-fusing ATPase / type: protein_or_peptide / ID: 1
Details: First 37 residues are expression tags. I80 is a covalently conjugated inhibitor to this chain.
Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Schistosoma mansoni (invertebrata)
Molecular weightTheoretical: 92.755594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFMCAL NANPSNDPSS GEKVKFHRLI VDEPVKDDNS VVYLSQAKMD SMNLFRGDT VLVKGKKRKE TVCVAIVDES CPDDKIRLNR CIRSNLRVKP GDIISIKSLP DILYGKRIHV LPIDDTIVGL T GNLYEAFL ...String:
MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSEFMCAL NANPSNDPSS GEKVKFHRLI VDEPVKDDNS VVYLSQAKMD SMNLFRGDT VLVKGKKRKE TVCVAIVDES CPDDKIRLNR CIRSNLRVKP GDIISIKSLP DILYGKRIHV LPIDDTIVGL T GNLYEAFL KPYFLAAYRP VHKGDIFIVR GGMRAVEFKV IETDPSPYCI VSPDTTIHTE GDPVKREDEE EKLNEIGYDD IG GCRKQLA QIKEMVELPL RHPQLFKAIG VKPPRGILLY GPPGTGKTLV ARAVANESGS FFFLINGPEI MSKLAGESES NLR KAFEEA EKNAPAIIFI DELDAIAPKR EKTHGEVERR IVSQLLTLMD GLKQRSHVIV MAATNRPNSV DPALRRFGRF DREI EIGIP DSIGRLEILR IHTRNIRLAE DVELEKIANE AHGHVGADLA SLCSEAALQQ IRNKMNLIDL EDDTIDAEVL NSLAV TMDD FRWALGKSNP SALRETTVEV PNVTWDDIGG LENVKRELQE LVQYPVEHPD KFLKFGMTPS KGVLFYGPPG CGKTLL AKA IANECQANFI SIKGPELLTM WFGESEANVR DIFDKARQAA PCVLFFDELD SIAKARGGSV GDAGGAADRV INQLLTE MD GMSAKKNVFI IGATNRPDII DGAILRPGRL DQLIYIPLPD EASRVNILKA NLRKSPIARD VDINFLAKAT QGFSGADL T EICQRACKQA IRESIEAEIR AESEKKNKPN AMEDDFDPVP EITRRHFEEA MRFARRSVTE NDVRKYEMFA QTLQQSRGI GNNFRFPGSD GSGIPTSTGG QGGGGSVYGS QNDAEDLYN

UniProtKB: vesicle-fusing ATPase

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Macromolecule #2: (2Z)-N-[2-(3-methylpyridin-2-yl)-1,3-benzoxazol-5-yl]-3-(pyridin-...

MacromoleculeName: (2Z)-N-[2-(3-methylpyridin-2-yl)-1,3-benzoxazol-5-yl]-3-(pyridin-4-yl)prop-2-enamide
type: ligand / ID: 2 / Number of copies: 6 / Formula: A1CGG
Molecular weightTheoretical: 356.377 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

Concentration1 mg/mL
BufferpH: 7.4
Details: 20mM Tris (pH 7.4), 180mM NaCl, 5mM MgCl2, and 1mM tris(2-carboxyethyl)phosphine (TCEP)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2272397
Details: Template picking using templates generated using CB-5083-bound map.
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

70961


Details: 2 of the same CB-5083-bound map.
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Homogenous refinement with C6 symmetry applied, and global and local CTF refinements. DeepEMhancer sharpened map was used for modeling.
Number images used: 823143
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC / Details: With C6 symmetry
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9p00


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsApo structure was docked and refined.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9p07:
Cryo-EM structure of S. Mansoni p97 bound to compound 804

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