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- PDB-9bji: Cryo-EM structure of apo NVL -

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Basic information

Entry
Database: PDB / ID: 9bji
TitleCryo-EM structure of apo NVL
Components
  • Nuclear valosin-containing protein-like
  • Substrate mimic
KeywordsTRANSLOCASE / Ribosome biogenesis / AAA+ ATPase
Function / homology
Function and homology information


regulation of protein localization to nucleolus / preribosome binding / telomerase holoenzyme complex / telomerase holoenzyme complex assembly / positive regulation of telomere maintenance / positive regulation of protein binding / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / nucleolus ...regulation of protein localization to nucleolus / preribosome binding / telomerase holoenzyme complex / telomerase holoenzyme complex assembly / positive regulation of telomere maintenance / positive regulation of protein binding / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
NVL2, nucleolin binding domain / NVL2, N-terminal domain superfamily / Nucleolin binding domain / : / 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 ...NVL2, nucleolin binding domain / NVL2, N-terminal domain superfamily / Nucleolin binding domain / : / 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 / Nuclear valosin-containing protein-like
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsCruz, V.E. / Erzberger, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
Robert A. Welch FoundationI-1422 United States
Robert A. Welch FoundationV-I-0002-20230731 United States
CitationJournal: To Be Published
Title: Dibenzothiazepinones are bioavailable inhibitors of NVL and cause p53-dependent apoptosis in cancer by blocking 60S ribosome assembly
Authors: Guo, H.H. / Tao, Y. / Cruz, V.E. / Fang, M. / Khivansara, V. / Xie, S. / Leach, A. / Rivera-Cancel, G. / Barrows, N. / Williams, N. / Aurora, A. / Erzberger, J.P. / De Brabander, J.K. / Nijhawan, D.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Substrate mimic
A: Nuclear valosin-containing protein-like
B: Nuclear valosin-containing protein-like
C: Nuclear valosin-containing protein-like
D: Nuclear valosin-containing protein-like
E: Nuclear valosin-containing protein-like
F: Nuclear valosin-containing protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)579,18524
Polymers574,4257
Non-polymers4,75917
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/peptide Substrate mimic


Mass: 3333.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Substrate mimic / Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein
Nuclear valosin-containing protein-like / NVLp / Nuclear VCP-like protein


Mass: 95181.992 Da / Num. of mol.: 6 / Mutation: E365Q,E682Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NVL, NVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15381
#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.: 8 / 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: apo NVL / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
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: OTHER / Nominal defocus max: 1900 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 1.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109860 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 38.66 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226229
ELECTRON MICROSCOPYf_angle_d0.443635522
ELECTRON MICROSCOPYf_chiral_restr0.03854124
ELECTRON MICROSCOPYf_plane_restr0.00354627
ELECTRON MICROSCOPYf_dihedral_angle_d11.654510249

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