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), 0.254 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Models: experimental
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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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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:  (by identity cutoff)  |  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), 0.254 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • 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