7B47

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Human p53DBD-R273H mutant bound to MQ: R273H-MQ (I)

PDB DOI: https://doi.org/10.2210/pdb7B47/pdb

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

Deposited: 2020-12-02 Released: 2021-12-08
Deposition Author(s): Degtjarik, O., Rozenberg, H., Shakked, Z.
Funding Organization(s): Aprea Therapeutics AB

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.202
R-Value Work: 0.178
R-Value Observed: 0.178

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ).

Degtjarik, O., Golovenko, D., Diskin-Posner, Y., Abrahmsen, L., Rozenberg, H., Shakked, Z.

(2021) Nat Commun 12: 7057-7057

PubMed: 34862374 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27142-6
Primary Citation of Related Structures:
6ZNC, 7B46, 7B47, 7B48, 7B49, 7B4A, 7B4B, 7B4C, 7B4D, 7B4E, 7B4F, 7B4G, 7B4H, 7B4N

PubMed Abstract:
In response to genotoxic stress, the tumor suppressor p53 acts as a transcription factor by regulating the expression of genes critical for cancer prevention. Mutations in the gene encoding p53 are associated with cancer development. PRIMA-1 and eprenetapopt (APR-246/PRIMA-1 ^MET) are small molecules that are converted into the biologically active compound, methylene quinuclidinone (MQ), shown to reactivate mutant p53 by binding covalently to cysteine residues. Here, we investigate the structural basis of mutant p53 reactivation by MQ based on a series of high-resolution crystal structures of cancer-related and wild-type p53 core domains bound to MQ in their free state and in complexes with their DNA response elements. Our data demonstrate that MQ binds to several cysteine residues located at the surface of the core domain. The structures reveal a large diversity in MQ interaction modes that stabilize p53 and its complexes with DNA, leading to a common global effect that is pertinent to the restoration of non-functional p53 proteins.

Organizational Affiliation

Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel.

Macromolecule Content

Total Structure Weight: 91.6 kDa
Atom Count: 6,741
Modelled Residue Count: 758
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	A, B, C, D	200	Homo sapiens	Mutation(s): 1 Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637
PHAROS: P04637 GTEx: ENSG00000141510
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04637
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QNN Query on QNN Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	I [auth B], K [auth B], M [auth C], Q [auth D]	(2~{S})-2-methyl-1-azabicyclo[2.2.2]octan-3-one C₈ H₁₃ N O LGOHLIRGPFPGKT-LURJTMIESA-N		Interactions Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain I [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain Q [auth D]
QN8 Query on QN8 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain R [auth D]	F [auth A] G [auth A] J [auth B] O [auth D] P [auth D] F [auth A], G [auth A], J [auth B], O [auth D], P [auth D], R [auth D]	(2~{R})-2-methyl-1-azabicyclo[2.2.2]octan-3-one C₈ H₁₃ N O LGOHLIRGPFPGKT-ZCFIWIBFSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], L [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain N [auth D]