9LA9 | pdb_00009la9

Munc13-4-Rab27a complex with GppNHp


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.38 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

Munc13-4 mediates tumor immune evasion by regulating the sorting and secretion of PD-L1 via exosomes.

Liu, C.Liu, D.Zheng, X.Guan, J.Zhou, X.Zhang, H.Wang, S.Li, Q.Lu, G.He, J.Ma, C.

(2025) Nat Commun 16: 9080-9080

  • DOI: https://doi.org/10.1038/s41467-025-64149-9
  • Primary Citation of Related Structures:  
    9LA9

  • PubMed Abstract: 

    Tumor-derived exosomes carry programmed death-ligand 1 (PD-L1), which binds programmed cell death protein 1 (PD-1) on T cells, suppressing immune responses locally and systemically. However, the mechanisms governing exosomal PD-L1 sorting and secretion remain elusive. Here, we identify Munc13-4 as a crucial regulator of this process. Deletion of Munc13-4 in breast tumors enhances T cell-mediated anti-tumor immunity, suppresses tumor growth, and improves the efficacy of immune checkpoint inhibitors. Mechanistically, Munc13-4 collaborates with hepatocyte growth factor-regulated tyrosine kinase substrate (HRS), Rab27, and SNAREs to facilitate PD-L1 sorting and secretion via exosomes. Cryogenic electron microscopy (cryo-EM) analysis of the Munc13-4-Rab27a complex provide structural insights into exosome secretion. Importantly, PD-L1 sorting relies on a ternary complex composed of Munc13-4, PD-L1 and HRS, which is regulated by interferon gamma (IFNγ) signaling. A designed peptide that disrupts Munc13-4-PD-L1 interaction impedes PD-L1 sorting, enhances antitumor immunity, and suppresses tumor growth, highlighting the therapeutic potential of targeting this pathway.


  • Organizational Affiliation
    • Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein unc-13 homolog D1,118Homo sapiensMutation(s): 0 
Gene Names: UNC13D
UniProt & NIH Common Fund Data Resources
Find proteins for Q70J99 (Homo sapiens)
Explore Q70J99 
Go to UniProtKB:  Q70J99
PHAROS:  Q70J99
GTEx:  ENSG00000092929 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70J99
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-27A263Homo sapiensMutation(s): 0 
Gene Names: RAB27ARAB27
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51159 (Homo sapiens)
Explore P51159 
Go to UniProtKB:  P51159
PHAROS:  P51159
GTEx:  ENSG00000069974 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51159
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
C [auth B]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32225024, 92254302
National Natural Science Foundation of China (NSFC)China2022YFA1206001
National Natural Science Foundation of China (NSFC)China32241021
National Natural Science Foundation of China (NSFC)China32170189
National Natural Science Foundation of China (NSFC)China3231163669
Other private2024A04J6348

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Data collection, Database references