9NYP | pdb_00009nyp

Cryo-EM structure of NVL bound the the MM927 inhibitor

PDB DOI: https://doi.org/10.2210/pdb9NYP/pdb
EM Map EMD-49941: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Homo sapiens, unidentified
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): Yes

Deposited: 2025-03-28 Released: 2026-04-29
Deposition Author(s): Cruz, V.E., Erzberger, J.P.
Funding Organization(s): Robert A. Welch Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9NYP

This is version 1.0 of the entry. See complete history.

Literature

Optimized dibenzothiazepinones activate the impaired ribosome biogenesis checkpoint and trigger p53-dependent apoptosis by inhibiting the 60S assembly factor NVL

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.

To be published.

Macromolecule Content

Total Structure Weight: 580.1 kDa
Atom Count: 26,022
Modeled Residue Count: 3,327
Deposited Residue Count: 5,160
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear valosin-containing protein-like	A, B, C, D, E A, B, C, D, E, F	856	Homo sapiens	Mutation(s): 2 Gene Names: NVL, NVL2
UniProt & NIH Common Fund Data Resources
Find proteins for O15381 (Homo sapiens) Explore O15381 Go to UniProtKB: O15381
PHAROS: O15381 GTEx: ENSG00000143748
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15381
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
polypeptide substrate mimic	G [auth P]	24	unidentified	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] L [auth B] M [auth B] P [auth C] H [auth A], I [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], T [auth D], U [auth D], X [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E]
A1B7F (Subject of Investigation/LOI) Query on A1B7F Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain Z [auth E]	Z [auth E]	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 C₂₆ H₁₈ F N₃ O₄ S RFCSFVZTHMAECY-UHFFFAOYSA-N		Interactions Focus chain Z [auth E] Interactions & Density Focus chain Z [auth E]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain Y [auth E]	Y [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Y [auth E] Interactions & Density Focus chain Y [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] N [auth B] O [auth B] R [auth C] J [auth A], K [auth A], N [auth B], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION	4.0.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-29

Deposition Author(s):

Erzberger, J.P.

Funding Organization	Location	Grant Number
Robert A. Welch Foundation	United States	I-1422
Robert A. Welch Foundation	United States	V-I-0002-20230731

Revision History (Full details and data files)

Version 1.0: 2026-04-29
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.