9I5E | pdb_00009i5e

A Coiled Coil Module Strategy for High-Resolution Cryo-EM Structures of Small Proteins for Drug Discovery

PDB DOI: https://doi.org/10.2210/pdb9I5E/pdb
EM Map EMD-52628: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, Lama glama
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-01-28 Released: 2025-11-12
Deposition Author(s): Samson, C., Dossou, I., Steinmetz, A., Kumar, A., Mathieu, M., Rak, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.77 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural determination of small proteins by cryo-EM using a coiled coil module strategy.

Camille, S., Irene, D., Anke, S., Anand, K., Magali, M., Alexey, R.

(2025) Sci Rep 15: 36800-36800

PubMed: 41120715 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-025-20608-3
Primary Citation Related Structures:
9I5E

PubMed Abstract:
Electron cryo-microscopy (Cryo-EM) has traditionally been used for structural determination of proteins larger than 50 kDa. Recently, various approaches, such as fusion to a scaffold or the use of DARPins-cages, have been developed to extend its application to smaller proteins. In this study, we determined the structure of the small protein target kRasG12C by fusing it to the coiled-coil motif APH ₂, which is targeted by several nanobodies. This method enabled us to achieve a structure with atomic details at a resolution of 3.7 Å. The kRasG12C structure was bound to the inhibitor drug MRTX849 and GDP, both clearly visible in the density map. This method is advantageous due to its ease of setup and applicability to other targets. Additionally, we investigated several other techniques that can be applied to small proteins, regardless of the presence of a terminal helix. These advancements demonstrate the potential of cryo-EM for detailed structural analysis of a wide range of protein targets, extending cryo-EM application for drug discovery.

Organizational Affiliation

Bio Structure and Biophysics at Integrated Drug Discovery, Sanofi R&D, Paris, France.

Macromolecule Content

Total Structure Weight: 76.2 kDa
Atom Count: 5,340
Modeled Residue Count: 652
Deposited Residue Count: 652
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas,APH2	A, D [auth B]	204	Homo sapiens	Mutation(s): 1 Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116 Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 26	B [auth M], C [auth N]	122	Lama glama	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M1X Query on M1X Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	{(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2S)-2-fluoropropanoyl]piperazin-2-yl}acetonitrile C₃₂ H₃₇ Cl F N₇ O₂ BQFJNAAUAQEWHZ-XWGVYQGASA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]