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- PDB-8yad: structure of SPG11-SPG15 complex -

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Basic information

Entry
Database: PDB / ID: 8yad
Titlestructure of SPG11-SPG15 complex
Components
  • Spatacsin
  • Zinc finger FYVE domain-containing protein 26
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


phagosome-lysosome fusion involved in apoptotic cell clearance / walking behavior / corticospinal tract morphogenesis / regulation of store-operated calcium entry / localization within membrane / autophagosome organization / vesicle transport along microtubule / phosphatidylinositol-3-phosphate binding / axon extension / axo-dendritic transport ...phagosome-lysosome fusion involved in apoptotic cell clearance / walking behavior / corticospinal tract morphogenesis / regulation of store-operated calcium entry / localization within membrane / autophagosome organization / vesicle transport along microtubule / phosphatidylinositol-3-phosphate binding / axon extension / axo-dendritic transport / motor neuron apoptotic process / cholesterol efflux / lysosome organization / motor behavior / neuromuscular junction development / synaptic vesicle transport / mitotic cytokinesis / skeletal muscle fiber development / axonogenesis / regulation of cytokinesis / protein catabolic process / double-strand break repair via homologous recombination / memory / protein import into nucleus / late endosome / midbody / cytoplasmic vesicle / chemical synaptic transmission / lysosome / early endosome / axon / lysosomal membrane / centrosome / dendrite / synapse / protein kinase binding / nucleolus / endoplasmic reticulum / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Zinc finger FYVE domain-containing protein 26 / Spatacsin / Spatacsin, C-terminal domain / Spatacsin C-terminus / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Zinc finger FYVE domain-containing protein 26 / Spatacsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.02 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 8, 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
B: Spatacsin
C: Zinc finger FYVE domain-containing protein 26


Theoretical massNumber of molelcules
Total (without water)564,1272
Polymers564,1272
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 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
#2: Protein Zinc finger FYVE domain-containing protein 26 / FYVE domain-containing centrosomal protein / FYVE-CENT / Spastizin


Mass: 284943.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZFYVE26, KIAA0321 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q68DK2
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: SPG11-SPG15 complex / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Molecular weightValue: 0.568 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: TFS 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: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234969 / Symmetry type: POINT

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