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- EMDB-44634: Cryo-EM structure of NVL bound the the MM017 inhibitor -

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Basic information

Entry
Database: EMDB / ID: EMD-44634
TitleCryo-EM structure of NVL bound the the MM017 inhibitor
Map data
Sample
  • Complex: NVL bound to MM017 inhibitor
    • Protein or peptide: Nuclear valosin-containing protein-like
    • Protein or peptide: Peptide substrate mimic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: N-[10-(2-methoxyethyl)-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepin-7-yl]furan-3-carboxamide
KeywordsRibosome biogenesis / AAA+ ATPase / TRANSLOCASE
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
Nuclear valosin-containing protein-like
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsCruz VE / Erzberger JP
Funding support United States, 2 items
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 HH / Tao Y / Cruz VE / Fang M / Khivansara V / Xie S / Leach A / Rivera-Cancel G / Barrows N / Williams N / Aurora A / Erzberger JP / De Brabander JK / Nijhawan D
History
DepositionApr 25, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44634.png

Downloads & links

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Map

FileDownload / File: emd_44634.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.05652284 - 0.12044344
Average (Standard dev.)0.000027817352 (±0.0042091967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44634_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44634_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NVL bound to MM017 inhibitor

EntireName: NVL bound to MM017 inhibitor
Components
  • Complex: NVL bound to MM017 inhibitor
    • Protein or peptide: Nuclear valosin-containing protein-like
    • Protein or peptide: Peptide substrate mimic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: N-[10-(2-methoxyethyl)-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepin-7-yl]furan-3-carboxamide

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Supramolecule #1: NVL bound to MM017 inhibitor

SupramoleculeName: NVL bound to MM017 inhibitor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nuclear valosin-containing protein-like

MacromoleculeName: Nuclear valosin-containing protein-like / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.181992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKPRPAGFVD NKLKQRVIQY LTSNKCGKYV DIGVLASDLQ RVYSIDYGRR KRNAFRIQVE KVFSIISSEK ELKNLTELED EHLAKRARQ GEEDNEYTES YSDDDSSMED YPDPQSANHM NSSLLSLYRK GNPDSVSNTP EMEQRETTSS TPRISSKTGS I PLKTPAKD ...String:
MKPRPAGFVD NKLKQRVIQY LTSNKCGKYV DIGVLASDLQ RVYSIDYGRR KRNAFRIQVE KVFSIISSEK ELKNLTELED EHLAKRARQ GEEDNEYTES YSDDDSSMED YPDPQSANHM NSSLLSLYRK GNPDSVSNTP EMEQRETTSS TPRISSKTGS I PLKTPAKD SEGGWFIDKT PSVKKDSFFL DLSCEKSNPK KPITEIQDSK DSSLLESDMK RKGKLKNKGS KRKKEDLQEV DG EIEAVLQ KKAKARGLEF QISNVKFEDV GGNDMTLKEV CKMLIHMRHP EVYHHLGVVP PRGVLLHGPP GCGKTLLAHA IAG ELDLPI LKVAAPEIVS GVSGESEQKL RELFEQAVSN APCIIFIDQI DAITPKREVA SKDMERRIVA QLLTCMDDLN NVAA TARVL VIGATNRPDS LDPALRRAGR FDREICLGIP DEASRERILQ TLCRKLRLPQ AFDFCHLAHL TPGFVGADLM ALCRE AAMC AVNRVLMKLQ EQQKKNPEME DLPSKGVQEE RLGTEPTSET QDELQRLLGL LRDQDPLSEE QMQGLCIELN DFIVAL SSV QPSAKREGFV TVPNVTWADI GALEDIREEL TMAILAPVRN PDQFKALGLV TPAGVLLAGP PGCGKTLLAK AVANESG LN FISVKGPELL NMYVGESERA VRQVFQRAKN SAPCVIFFDQ VDALCPRRSD RETGASVRVV NQLLTEMDGL EARQQVFI M AATNRPDIID PAILRPGRLD KTLFVGLPPP ADRLAILKTI TKNGTKPPLD ADVNLEAIAG DLRCDCYTGA DLSALVREA SICALRQEMA RQKSGNEKGE LKVSHKHFEE AFKKVRSSIS KKDQIMYERL QESLSR

UniProtKB: Nuclear valosin-containing protein-like

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Macromolecule #2: Peptide substrate mimic

MacromoleculeName: Peptide substrate mimic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.33354 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
HHHHHHHHHH HHHHHHHHHH HHHH

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 9 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: N-[10-(2-methoxyethyl)-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiaz...

MacromoleculeName: N-[10-(2-methoxyethyl)-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepin-7-yl]furan-3-carboxamide
type: ligand / ID: 5 / Number of copies: 2 / Formula: A1AP0
Molecular weightTheoretical: 394.444 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100118
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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