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- EMDB-39094: AP5 complex bound to SPG11-SPG15 -

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Basic information

Entry
Database: EMDB / ID: EMD-39094
TitleAP5 complex bound to SPG11-SPG15
Map data
Sample
  • Complex: AP5 complex bound to SPG11-SPG15
    • Protein or peptide: AP-5 complex subunit zeta-1
    • Protein or peptide: AP-5 complex subunit beta-1
    • Protein or peptide: AP-5 complex subunit sigma-1
    • Protein or peptide: AP-5 complex subunit mu-1
    • Protein or peptide: Spatacsin
KeywordsComplex / TRANSPORT PROTEIN
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 / lysosome organization / motor behavior / 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 speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsSu M-Y
Funding support China, 1 items
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, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39094.png

Downloads & links

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Map

FileDownload / File: emd_39094.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.624649 - 1.2771893
Average (Standard dev.)-0.00079125346 (±0.03173428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer map highRes model

Fileemd_39094_additional_1.map
AnnotationdeepEMhancer map highRes model
Projections & Slices
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Additional map: deepEMhancer map tightTarget model

Fileemd_39094_additional_2.map
AnnotationdeepEMhancer map tightTarget model
Projections & Slices
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Half map: #1

Fileemd_39094_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39094_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : AP5 complex bound to SPG11-SPG15

EntireName: AP5 complex bound to SPG11-SPG15
Components
  • Complex: AP5 complex bound to SPG11-SPG15
    • Protein or peptide: AP-5 complex subunit zeta-1
    • Protein or peptide: AP-5 complex subunit beta-1
    • Protein or peptide: AP-5 complex subunit sigma-1
    • Protein or peptide: AP-5 complex subunit mu-1
    • Protein or peptide: Spatacsin

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Supramolecule #1: AP5 complex bound to SPG11-SPG15

SupramoleculeName: AP5 complex bound to SPG11-SPG15 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: AP-5 complex subunit zeta-1

MacromoleculeName: AP-5 complex subunit zeta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 89.574422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFSAGAESL LHQAREIQDE ELRRFCSRVT KLLQEAPGPA TVDALQRLFL IVSATKYPRR LEKMCVDLLQ TTLCLPASPE QLQVLCAAI LREMSPFNDL ALSCDHTPNT RQLSLVASVL LAQGDRKGEI RCVSQRIFKI LENRQPEGPS VRPLLPILSK V IGLAPGIL ...String:
MAFSAGAESL LHQAREIQDE ELRRFCSRVT KLLQEAPGPA TVDALQRLFL IVSATKYPRR LEKMCVDLLQ TTLCLPASPE QLQVLCAAI LREMSPFNDL ALSCDHTPNT RQLSLVASVL LAQGDRKGEI RCVSQRIFKI LENRQPEGPS VRPLLPILSK V IGLAPGIL MEDQTNLLSK RLVDWLRYAS IQQGLPYSGG FFSTPRTRQP GPITEVDGAV ASDFFTVLST GQHFTEDQWV NM QAFSMLR KWLLHSGPED PCSPDADDKS ELEGSTLSVL SAASTASRLL PPRERLREVA FEYCQRLLEQ SNRRALRKGD SDL QKACLV EAVSVLDVLC RQDPSFLYRT LSCLKALHRR LGEDPGSERA LVPLAQFFLN HGEAAAMDAE AVYGQLLRGL PSER FHSPT LAFEVIHFCT HNLALFDSHF LSLLRLSFPS LFKFLAWNSP PLTAEFVVLL PALVDAGTAV EMLHALLDLP CLTAA LDLQ LRSTQTPSER LLWDISLRVP SCLEAFQDPQ FQGLFRHLLR TKASGSTERL TPLHQVLKPM ASCARVTQCA EAVPVL LQA FFSAVTQTAD GALINQLALL LLERSDSLYP VPQYEARVHG VLSSQLLVLC KLKPSLVVEL SRELLEFVGS VSSIHSR AS VFTCVVWAIG EYLSVTWDKR CTAEQINKFF EALEALLFEV TQSRPLADLP CCPPEVVTAL MTTLTKLASR SQDLIPRV S LFLSKMRTLA QNPATSSVHS EEGAESIRTR ASELLTLLKM PSVAQFVFTP PAGVCQPRYH RDTNVALPLA LRTVSRLVE KEAGLLPG

UniProtKB: AP-5 complex subunit zeta-1

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Macromolecule #2: AP-5 complex subunit beta-1

MacromoleculeName: AP-5 complex subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.038109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGPLSRDAWA QRLGAFRASP SAFMAGPEGE DLGRDLLSDL RSEKLSEQTK VSLLALSMEY PAQLWPDASA AEVAATSLLD TLVLLPPRP SALRRPLLLA ATTALAAGGA LGPTSGASCR LLPLLLGLAA GSDLGRGFVP ASEQRPLQAT ACECLRELES C KPGLLGGS ...String:
MGPLSRDAWA QRLGAFRASP SAFMAGPEGE DLGRDLLSDL RSEKLSEQTK VSLLALSMEY PAQLWPDASA AEVAATSLLD TLVLLPPRP SALRRPLLLA ATTALAAGGA LGPTSGASCR LLPLLLGLAA GSDLGRGFVP ASEQRPLQAT ACECLRELES C KPGLLGGS LGLLRGLLGQ EGPVQPLSLL LALALRNTLV LQSRVGAGLG GLLTDKVSPT GGGPWDWTLV EEGDGRLQPQ AP SWPAAEE GEGERSLTAR EHSPEEAREL RAAVIQLLDT SYLLTPVAQA QLLWLLGWAL RGLQGQPPAL FKPQLVRLLG TAQ LTLLHA MLALKAAFGE ALFTAQDEAL LLRRLTLAAQ HPALPPPTHL FYLHCVLSFP ENWPLGPEGE EAAPLLLGPQ LCRG LLPSL LHDPMALLAR LHLLCLLCAE EEEEEKGQLP SPRHYLEELL AGLRQRAALD GGPRALATLC FQASYLVACC LAGQP TVLT PLIHGLAQLY QARPMLAPHF VDLLDQVDSE LREPLKVVLR QVVVSRPGRD EALCWHLQML AKVADGDAQS ATLNFL QAA AAHCTNWDLQ QGLLRVCRAL LRAGVRGGLV DLLQVLARQL EDPDGRDHAR LYYILLAHLA APKLGVALGP SLAAPAL AS SLVAENQGFV AALMVQEAPA LVRLSLGSHR VKGPLPVLKL QPEALEPIYS LELRFRVEGQ LYAPLEAVHV PCLCPGRP A RPLLLPLQPR CPAPARLDVH ALYTTSTGLT CHAHLPPLFV NFADLFLPFP QPPEGAGLGF FEELWDSCLP EGAESRVWC PLGPQGLEGL VSRHLEPFVV VAQPPTSYCV AIHLPPDSKL LLRLEAALAD GVPVALRTDD WAVLPLAGDY LRGLAAAV

UniProtKB: AP-5 complex subunit beta-1

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Macromolecule #3: AP-5 complex subunit sigma-1

MacromoleculeName: AP-5 complex subunit sigma-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.550984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVHAFLIHTL RAPNTEDTGL CRVLYSCVFG AEKSPDDPRP HGAERDRLLR KEQILAVARQ VESMCRLQQQ ASGRPPMDLQ PQSSDEQVP LHEAPRGAFR LAAENPFQEP RTVVWLGVLS LGFALVLDAH ENLLLAEGTL RLLTRLLLDH LRLLAPSTSL L LRADRIEG ...String:
MVHAFLIHTL RAPNTEDTGL CRVLYSCVFG AEKSPDDPRP HGAERDRLLR KEQILAVARQ VESMCRLQQQ ASGRPPMDLQ PQSSDEQVP LHEAPRGAFR LAAENPFQEP RTVVWLGVLS LGFALVLDAH ENLLLAEGTL RLLTRLLLDH LRLLAPSTSL L LRADRIEG ILTRFLPHGQ LLFLNDQFVQ GLEKEFSAAW PR

UniProtKB: AP-5 complex subunit sigma-1

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Macromolecule #4: AP-5 complex subunit mu-1

MacromoleculeName: AP-5 complex subunit mu-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 54.393285 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALRAVWLIR HEPGTPLGGT VRFSRRYPTV EKRAKAFNGM TYVPVPEDGP FLRALLFQLR LLDDDKDFME RRDGCSRINK TSIYGLSVG GEELWPVIAF LRDSMIYASV PLVEQALSPR PPLISISGVS QGLELLLGIQ DFLYSSQKND TDLHTKLSQL P DLLLQACP ...String:
MALRAVWLIR HEPGTPLGGT VRFSRRYPTV EKRAKAFNGM TYVPVPEDGP FLRALLFQLR LLDDDKDFME RRDGCSRINK TSIYGLSVG GEELWPVIAF LRDSMIYASV PLVEQALSPR PPLISISGVS QGLELLLGIQ DFLYSSQKND TDLHTKLSQL P DLLLQACP LGTLLDANLQ NSLNSINSVS VTQPQKQPAW KVGAYKGKAQ ISISITETVK CMQYGKQDIA DTWQVAGTVA CK CDLEGVM PAVTISLSLP TNGSPLQDII VHPCVTSLDS AILTSSSIDT MDDSAFSGPY KFPFTPPLES FNLCHYTSQV PVP PILGSY HMKEEGVQLK VTVNFKLHES VRNNFEVCEA HIPFYNRGPI THLEYKASFG QLEVFREKSL LVWIIGQKFP KSME ISLSG TLTFGVKGHN KQPFDHICIG NTAYIKLNFR IADYTLTGCY ADQHSVQVFA SGKPKISAYR KLISSDYYIW NSKAP APVT YASLLP

UniProtKB: AP-5 complex subunit mu-1

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Macromolecule #5: Spatacsin

MacromoleculeName: Spatacsin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.115113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA GSLQVLSLTP GSRGGGRCCL EGPFWHFLW EDSRNSSTPT EKPKLLALGE NYELLIYEFN LKDGRCDATI LYSCSREALQ KLIDDQDISI SLLSLRILSF H NNTSLLFI ...String:
MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA GSLQVLSLTP GSRGGGRCCL EGPFWHFLW EDSRNSSTPT EKPKLLALGE NYELLIYEFN LKDGRCDATI LYSCSREALQ KLIDDQDISI SLLSLRILSF H NNTSLLFI NKCVILHIIF PERDAAIRVL NCFTLPLPAQ AVDMIIDTQL CRGILFVLSS LGWIYIFDVV DGTYVAHVDL AL HKEDMCN EQQQEPAKIS SFTSLKVSQD LDVAVIVSSS NSAVALNLNL YFRQHPGHLL CERILEDLPI QGPKGVDEDD PVN SAYNMK LAKFSFQIDR SWKAQLSSLN ETIKNSKLEV SCCAPWFQDI LHLESPESGN HSTSVQSWAF IPQDIMHGQY NVLQ KDHAK TSDPGRSWKI MHISEQEEPI ELKCVSVTGF TALFTWEVER MGYTITLWDL ETQGMQCFSL GTKCIPVDSS GDQQL CFVL TENGLSLILF GLTQEEFLNR LMIHGSASTV DTLCHLNGWG R

UniProtKB: Spatacsin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2386 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 399340
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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