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- PDB-9nyp: Cryo-EM structure of NVL bound the the MM927 inhibitor -

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Basic information

Entry
Database: PDB / ID: 9nyp
TitleCryo-EM structure of NVL bound the the MM927 inhibitor
Components
  • Nuclear valosin-containing protein-like
  • polypeptide substrate mimic
KeywordsTRANSLOCASE / Ribosome biogenesis / AAA+ ATPase
Function / homology
Function and homology information


regulation of protein localization to nucleolus / preribosome binding / telomerase holoenzyme complex / positive regulation of protein binding / telomerase holoenzyme complex assembly / positive regulation of telomere maintenance / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / nucleolus ...regulation of protein localization to nucleolus / preribosome binding / telomerase holoenzyme complex / positive regulation of protein binding / telomerase holoenzyme complex assembly / positive regulation of telomere maintenance / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
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'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Nuclear valosin-containing protein-like
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 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: Optimized dibenzothiazepinones activate the impaired ribosome biogenesis checkpoint and trigger p53-dependent apoptosis by inhibiting the 60S assembly factor NVL
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
DepositionMar 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 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
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
P: polypeptide substrate mimic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)580,09926
Polymers574,4257
Non-polymers5,67419
Water43224
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

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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFP

#1: Protein
Nuclear valosin-containing protein-like / NVLp / Nuclear VCP-like protein


Mass: 95181.992 Da / Num. of mol.: 6 / Mutation: E366Q,E683Q
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
#2: Protein/peptide polypeptide substrate mimic


Mass: 3333.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 43 molecules

#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
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-A1B7F / N-[10-(but-2-yn-1-yl)-3-fluoro-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepin-7-yl]-3-methyl-2-oxo-2,3-dihydro-1,3-benzoxazole-5-carboxamide


Mass: 487.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H18FN3O4S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

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: NVL bound to MM927 inhibitor / 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 software
IDNameVersionCategory
1RELION4.0.1particle selection
2PHENIX1.21.2_5419model refinement
5GctfCTF correction
10RELION4.0.1initial Euler assignment
11RELION4.0.1final Euler assignment
12RELION4.0.1classification
13RELION4.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7425878
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193335 / Symmetry type: POINT
RefinementCross valid method: NONE

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