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- PDB-8yah: full length AP5 complex bound to SPG11-SPG15 -

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Basic information

Entry
Database: PDB / ID: 8yah
Titlefull length AP5 complex bound to SPG11-SPG15
Components
  • AP-5 complex subunit beta-1
  • AP-5 complex subunit mu-1
  • AP-5 complex subunit sigma-1
  • AP-5 complex subunit zeta-1
  • Spatacsin
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


AP-5 adaptor complex / phagosome-lysosome fusion involved in apoptotic cell clearance / late endosome to Golgi transport / AP-type membrane coat adaptor complex / walking behavior / corticospinal tract morphogenesis / regulation of store-operated calcium entry / lysosomal protein catabolic process / localization within membrane / autophagosome organization ...AP-5 adaptor complex / phagosome-lysosome fusion involved in apoptotic cell clearance / late endosome to Golgi transport / AP-type membrane coat adaptor complex / walking behavior / corticospinal tract morphogenesis / regulation of store-operated calcium entry / lysosomal protein catabolic process / localization within membrane / autophagosome organization / vesicle transport along microtubule / axon extension / axo-dendritic transport / motor neuron apoptotic process / cholesterol efflux / endosomal transport / motor behavior / lysosome organization / neuromuscular junction development / synaptic vesicle transport / axon development / Golgi organization / autophagosome assembly / skeletal muscle fiber development / vesicle-mediated transport / axonogenesis / intracellular protein transport / protein catabolic process / double-strand break repair via homologous recombination / memory / autophagy / protein import into nucleus / late endosome membrane / late endosome / protein transport / cytoplasmic vesicle / gene expression / chemical synaptic transmission / lysosome / nuclear speck / axon / lysosomal membrane / synapse / dendrite / protein kinase binding / nucleolus / endoplasmic reticulum / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
AP-5 complex subunit zeta-1 / AP-5 complex subunit sigma-1 / AP-5 complex subunit beta-1 / AP-5 complex subunit mu-1 / : / : / : / : / : / AP-5 complex subunit, vesicle trafficking ...AP-5 complex subunit zeta-1 / AP-5 complex subunit sigma-1 / AP-5 complex subunit beta-1 / AP-5 complex subunit mu-1 / : / : / : / : / : / AP-5 complex subunit, vesicle trafficking / AP-5 complex subunit sigma-1 / AP-5 complex subunit beta-1, N-terminal / AP5B1, middle domain / AP-5 complex subunit beta-1, beta-barrel / AP5B1, C-terminal / Spatacsin / Spatacsin, C-terminal domain / Spatacsin C-terminus / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Armadillo-type fold
Similarity search - Domain/homology
AP-5 complex subunit beta-1 / AP-5 complex subunit zeta-1 / AP-5 complex subunit mu-1 / Spatacsin / AP-5 complex subunit sigma-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSu, M.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for membrane remodeling by the AP5-SPG11-SPG15 complex.
Authors: Xinyi Mai / Yang Wang / Xi Wang / Ming Liu / Fei Teng / Zheng Liu / Ming-Yuan Su / Goran Stjepanovic /
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 ...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.
History
DepositionFeb 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-5 complex subunit zeta-1
B: AP-5 complex subunit beta-1
C: AP-5 complex subunit sigma-1
E: AP-5 complex subunit mu-1
D: Spatacsin


Theoretical massNumber of molelcules
Total (without water)539,7395
Polymers539,7395
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein AP-5 complex subunit zeta-1 / Adaptor-related protein complex 5 zeta subunit


Mass: 89574.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap5z1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q3U829
#2: Protein AP-5 complex subunit beta-1 / Adaptor-related protein complex 5 beta subunit


Mass: 94038.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP5B1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q2VPB7
#3: Protein AP-5 complex subunit sigma-1 / Adaptor-related protein complex 5 sigma subunit


Mass: 22550.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP5S1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NUS5
#4: Protein AP-5 complex subunit mu-1 / Adaptor-related protein complex 5 subunit mu-1


Mass: 54393.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap5m1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8BJ63
#5: Protein Spatacsin / Spastic paraplegia 11 protein


Mass: 279182.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPG11 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q96JI7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: full length AP5 complex bound to SPG11-SPG15 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.826 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.2386 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 586806 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00914419
ELECTRON MICROSCOPYf_angle_d1.03319859
ELECTRON MICROSCOPYf_dihedral_angle_d4.8812299
ELECTRON MICROSCOPYf_chiral_restr0.0452522
ELECTRON MICROSCOPYf_plane_restr0.0062641

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