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- EMDB-49941: Cryo-EM structure of NVL bound the the MM927 inhibitor -

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Basic information

Entry
Database: EMDB / ID: EMD-49941
TitleCryo-EM structure of NVL bound the the MM927 inhibitor
Map data
Sample
  • Complex: NVL bound to MM927 inhibitor
    • Protein or peptide: Nuclear valosin-containing protein-like
    • Protein or peptide: polypeptide substrate mimic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 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
  • Ligand: water
KeywordsRibosome biogenesis / AAA+ ATPase / TRANSLOCASE
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
Nuclear valosin-containing protein-like
Similarity search - Component
Biological speciesHomo sapiens (human) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 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: Optimized dibenzothiazepinones activate the impaired ribosome biogenesis checkpoint and trigger p53-dependent apoptosis by inhibiting the 60S assembly factor NVL
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
DepositionMar 28, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49941.png

Downloads & links

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Map

FileDownload / File: emd_49941.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 297.72 Å		0.83 Å/pix.
x 360 pix.
= 297.72 Å		0.83 Å/pix.
x 360 pix.
= 297.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy SOFTWARE: 0.0053
Minimum - Maximum-0.022142455 - 0.045227863
Average (Standard dev.)0.0000024628548 (±0.0013724593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49941_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_49941_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 MM927 inhibitor

EntireName: NVL bound to MM927 inhibitor
Components
  • Complex: NVL bound to MM927 inhibitor
    • Protein or peptide: Nuclear valosin-containing protein-like
    • Protein or peptide: polypeptide substrate mimic
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 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
  • Ligand: water

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Supramolecule #1: NVL bound to MM927 inhibitor

SupramoleculeName: NVL bound to MM927 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: polypeptide substrate mimic

MacromoleculeName: polypeptide substrate mimic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 3.33354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #6: N-[10-(but-2-yn-1-yl)-3-fluoro-11-oxo-10,11-dihydrodibenzo[b,f][1...

MacromoleculeName: 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
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1B7F
Molecular weightTheoretical: 487.502 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Particle selectionNumber selected: 7425878
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

44633

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 193335
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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