8YAH | pdb_00008yah

full length AP5 complex bound to SPG11-SPG15


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for membrane remodeling by the AP5-SPG11-SPG15 complex.

Mai, X.Wang, Y.Wang, X.Liu, M.Teng, F.Liu, Z.Su, M.Y.Stjepanovic, G.

(2025) Nat Struct Mol Biol 32: 1334-1346

  • DOI: https://doi.org/10.1038/s41594-025-01500-0
  • Primary Citation of Related Structures:  
    8YAB, 8YAD, 8YAH

  • PubMed Abstract: 

    The human spastizin (spastic paraplegia 15, SPG15) and spatacsin (spastic paraplegia 11, SPG11) complex is involved in the formation of lysosomes, and mutations in these two proteins are linked with hereditary autosomal-recessive spastic paraplegia. SPG11-SPG15 can cooperate with the fifth adaptor protein complex (AP5) involved in membrane sorting of late endosomes. We employed cryogenic-electron microscopy and in silico predictions to investigate the structural assemblies of the SPG11-SPG15 and AP5-SPG11-SPG15 complexes. The W-shaped SPG11-SPG15 intertwined in a head-to-head fashion, and the N-terminal region of SPG11 is required for AP5 complex interaction and assembly. The AP5 complex is in a super-open conformation. Our findings reveal that the AP5-SPG11-SPG15 complex can bind PI3P molecules, sense membrane curvature and drive membrane remodeling in vitro. These studies provide insights into the structure and function of the spastic paraplegia AP5-SPG11-SPG15 complex, which is essential for the initiation of autolysosome tubulation.


  • Organizational Affiliation
    • Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-5 complex subunit zeta-1808Mus musculusMutation(s): 0 
Gene Names: Ap5z1
UniProt & NIH Common Fund Data Resources
Find proteins for Q3U829 (Mus musculus)
Explore Q3U829 
Go to UniProtKB:  Q3U829
IMPC:  MGI:1924908
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3U829
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP-5 complex subunit beta-1878Homo sapiensMutation(s): 0 
Gene Names: AP5B1
UniProt & NIH Common Fund Data Resources
Find proteins for Q2VPB7 (Homo sapiens)
Explore Q2VPB7 
Go to UniProtKB:  Q2VPB7
PHAROS:  Q2VPB7
GTEx:  ENSG00000254470 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2VPB7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AP-5 complex subunit sigma-1200Homo sapiensMutation(s): 0 
Gene Names: AP5S1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUS5 (Homo sapiens)
Explore Q9NUS5 
Go to UniProtKB:  Q9NUS5
PHAROS:  Q9NUS5
GTEx:  ENSG00000125843 
Entity Groups  
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UniProt GroupQ9NUS5
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-5 complex subunit mu-1D [auth E]490Mus musculusMutation(s): 0 
Gene Names: Ap5m1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BJ63 (Mus musculus)
Explore Q8BJ63 
Go to UniProtKB:  Q8BJ63
IMPC:  MGI:1921635
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UniProt GroupQ8BJ63
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SpatacsinE [auth D]2,443Homo sapiensMutation(s): 0 
Gene Names: SPG11
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JI7 (Homo sapiens)
Explore Q96JI7 
Go to UniProtKB:  Q96JI7
PHAROS:  Q96JI7
GTEx:  ENSG00000104133 
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UniProt GroupQ96JI7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-03-26 
  • Deposition Author(s): Su, M.-Y.

Funding OrganizationLocationGrant Number
Other governmentChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection
  • Version 1.3: 2025-08-27
    Changes: Data collection, Database references