9C1B

Crystal structure of GDP-bound human M-RAS protein in crystal form II

PDB DOI: https://doi.org/10.2210/pdb9C1B/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-28 Released: 2024-09-11
Deposition Author(s): Bester, S.M., Abrahamsen, R., Samora, L.R., Wu, W.-I., Mou, T.-C.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.247
R-Value Work: 0.199
R-Value Observed: 0.202

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the GDP-bound human M-RAS protein in two crystal forms.

Bester, S.M., Abrahamsen, R., Rodrigues Samora, L., Wu, W.I., Mou, T.C.

(2024) Acta Crystallogr F Struct Biol Commun 80: 220-227

PubMed: 39196705 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X24007969
Primary Citation of Related Structures:
9C1A, 9C1B

PubMed Abstract:
M-RAS plays a crucial role in the RAF-MEK signaling pathway. When activated by GTP, M-RAS forms a complex with SHOC2 and PP1C, initiating downstream RAF-MEK signal transduction. In this study, the crystal structure of the GDP-bound human M-RAS protein is presented with two forms of crystal packing. Both the full-length and truncated human M-RAS structures aligned well with the high-confidence section of the AlphaFold2-predicted structure with low r.m.s.d., except for the Switch regions. Despite high sequence similarity to the available mouse M-RAS structure, the full-length human M-RAS structure exhibits unique crystal packing. This inactive human M-RAS structure could offer novel insights for the design of selective compounds targeting M-RAS.

Organizational Affiliation

Pfizer Boulder Research and Development, 3200 Walnut Street, Boulder, CO 80301, USA.

Macromolecule Content

Total Structure Weight: 103.96 kDa
Atom Count: 5,932
Modelled Residue Count: 667
Deposited Residue Count: 876
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein M-Ras	A, B, C, D	219	Homo sapiens	Mutation(s): 0 Gene Names: MRAS, RRAS3 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O14807 (Homo sapiens) Explore O14807 Go to UniProtKB: O14807
PHAROS: O14807 GTEx: ENSG00000158186
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14807
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	F [auth A], J [auth B], M [auth C], Q [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C]	H [auth A], O [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], I [auth B], L [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]