9MEZ | pdb_00009mez

Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.255 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.214 (Depositor) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9MEZ

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural basis for LZTR1 recognition of RAS GTPases for degradation.

Dharmaiah, S.Bonsor, D.A.Mo, S.P.Fernandez-Cabrera, A.Chan, A.H.Messing, S.Drew, M.Vega, M.Nissley, D.V.Esposito, D.Castel, P.Simanshu, D.K.

(2025) Science 389: 1112-1117

  • DOI: https://doi.org/10.1126/science.adv7088
  • Primary Citation Related Structures: 
    9MEY, 9MEZ, 9MF0, 9MF1

  • PubMed Abstract: 

    The RAS family of small guanosine triphosphatases (GTPases) are tightly regulated signaling molecules that are further modulated by ubiquitination and proteolysis. Leucine Zipper-like Transcription Regulator 1 (LZTR1), a substrate adapter of the Cullin-3 RING E3 ubiquitin ligase, binds specific RAS GTPases and promotes their ubiquitination and proteasomal degradation. We present structures of LZTR1 Kelch domains bound to RIT1, MRAS, and KRAS, revealing interfaces that govern RAS isoform selectivity and nucleotide specificity. Biochemical and structural analyses of disease-associated Kelch domain mutations revealed three types of alterations: impaired substrate interaction, loop destabilization, and blade-blade repulsion. In cellular and mouse models, mutations disrupting substrate binding phenocopied LZTR1 loss, underscoring its substrate specificity. These findings define RAS recognition mechanisms by LZTR1 and suggest a molecular glue strategy to degrade oncogenic KRAS.


  • Organizational Affiliation
    • National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 289.62 kDa 
  • Atom Count: 19,477 
  • Modeled Residue Count: 2,444 
  • Deposited Residue Count: 2,520 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein M-Ras
A, C, E, G, I
182Homo sapiensMutation(s): 0 
Gene Names: MRASRRAS3
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14807
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-zipper-like transcriptional regulator 1
B, D, F, H, J
322Homo sapiensMutation(s): 0 
Gene Names: LZTR1TCFL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N653 (Homo sapiens)
Explore Q8N653 
Go to UniProtKB:  Q8N653
PHAROS:  Q8N653
GTEx:  ENSG00000099949 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N653
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
K [auth A],
N [auth C],
Q [auth E],
T [auth G],
X [auth I]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MLA

Query on MLA



Download:Ideal Coordinates CCD File
P [auth D],
S [auth E],
W [auth H]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
V [auth G]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT

Query on FMT



Download:Ideal Coordinates CCD File
M [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
L [auth A],
O [auth C],
R [auth E],
U [auth G],
Y [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.255 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.214 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.764α = 90
b = 110.788β = 94.53
c = 223.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States75N91019D00024

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references