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- EMDB-39096: structure of SPG11-SPG15 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39096
Titlestructure of SPG11-SPG15 complex
Map data
Sample
  • Complex: SPG11-SPG15 complex
    • Protein or peptide: Zinc finger FYVE domain-containing protein 26
    • Protein or peptide: Spatacsin
KeywordsComplex / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 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_39096.png

Downloads & links

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Map

FileDownload / File: emd_39096.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 800 pix.
= 680. Å		0.85 Å/pix.
x 800 pix.
= 680. Å		0.85 Å/pix.
x 800 pix.
= 680. 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: 0.08
Minimum - Maximum-0.26816913 - 1.1026474
Average (Standard dev.)-0.000477708 (±0.016051833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 680.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepemhancer map

Fileemd_39096_additional_1.map
Annotationdeepemhancer map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_39096_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39096_half_map_2.map
Projections & Slices
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Sample components

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Entire : SPG11-SPG15 complex

EntireName: SPG11-SPG15 complex
Components
  • Complex: SPG11-SPG15 complex
    • Protein or peptide: Zinc finger FYVE domain-containing protein 26
    • Protein or peptide: Spatacsin

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Supramolecule #1: SPG11-SPG15 complex

SupramoleculeName: SPG11-SPG15 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 568 KDa

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Macromolecule #1: Spatacsin

MacromoleculeName: Spatacsin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 279.182594 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 RCSIPIHALE AGIENRQLDT VNFFLKSKEN LFNPSS KSS VSDQFDHLSS HLYLRNVEEL IPALDLLCSA IRESYSEPQS KHFSEQLLNL TLSFLNNQIK ELFIHTEELD EHLQKGV NI LTSYINELRT FMIKFPWKLT DAIDEYDVHE NVPKVKESNI WKKLSFEEVI ASAILNNKIP EAQTFFRIDS HSAQKLEE L IGIGLNLVFD NLKKNNIKEA SELLKNMGFD VKGQLLKICF YTTNKNIRDF LVEILKEKNY FSEKEKRTID FVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTA RHDWLNIILW IGEFQTQHSY ASLQQNKWPL LTVDVINQNT SCNNYMRNEI LDKLARNGVF LASELEDFEC F LLRLSRIG GVIQDTLPVQ NYKTKEGWDF HSQFILYCLE HSLQHLLYVY LDCYKLSPEN CPFLEKKELH EAHPWFEFLV QC RQVASNL TDPKLIFQAS LANAQILIPT NQASVSSMLL EGHTLLALAT TMYSPGGVSQ VVQNEENENC LKKVDPQLLK MAL TPYPKL KTALFPQCTP PSVLPSDITI YHLIQSLSPF DPSRLFGWQS ANTLAIGDAW SHLPHFSSPD LVNKYAIVER LNFA YYLHN GRPSFAFGTF LVQELIKSKT PKQLIQQVGN EAYVIGLSSF HIPSIGAACV CFLELLGLDS LKLRVDMKVA NIILS YKCR NEDAQYSFIR ESVAEKLSKL ADGEKTTTEE LLVLLEEGTW NSIQQQEIKR LSSESSSQWA LVVQFCRLHN MKLSIS YLR ECAKANDWLQ FIIHSQLHNY HPAEVKSLIQ YFSPVIQDHL RLAFENLPSV PTSKMDSDQV CNKCPQELQG SKQEMTD LF EILLQCSEEP DSWHWLLVEA VKQQAPILSV LASCLQGASA ISCLCVWIIT SVEDNVATEA MGHIQDSTED HTWNLEDL S VIWRTLLTRQ KSKTLIRGFQ LFFKDSPLLL VMEMYELCMF FRNYKEAEAK LLEFQKSLET LNTAATKVHP VIPAMWLED QVCFLLKLML QQCKTQYELG KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL QTDGQFALA RRVAELAELP VDNLVIKEIT QEMQTLKHIE QWSLKQARID FWKKCHENFK KNSISSKAAS SFFSTQAHVA C EHPTGWSS MEERHLLLTL AGHWLAQEDV VPLDKLEELE KQIWLCRITQ HTLGRNQEET EPRFSRQIST SGELSFDSLA SE FSFSKLA ALNTSKYLEL NSLPSKETCE NRLDWKEQES LNFLIGRLLD DGCVHEASRV CRYFHFYNPD VALVLHCRAL ASG EASMED LHPEIHALLQ SAELLEEEAP DIPLRRVHST SSLDSQKFVT VPSSNEVVTN LEVLTSKCLH GKNYCRQVLC LYDL AKELG CSYTDVAAQD GEAMLRKILA SQQPDRCKRA QAFISTQGLK PDTVAELVAE EVTRELLTSS QGTGHKQMFN PTEES QTFL QLTTLCQDRT LVGMKLLDKI SSVPHGELSC TTELLILAHH CFTLTCHMEG IIRVLQAAHM LTDNHLAPSE EYGLVV RLL TGIGRYNEMT YIFDLLHKKH YFEVLMRKKL DPSGTLKTAL LDYIKRCRPG DSEKHNMIAL CFSMCREIGE NHEAAAR IQ LKLIESQPWE DSLKDGHQLK QLLLKALTLM LDAAESYAKD SCVRQAQHCQ RLTKLITLQI HFLNTGQNTM LINLGRHK L MDCILALPRF YQASIVAEAY DFVPDWAEIL YQQVILKGDF NYLEEFKQQR LLKSSIFEEI SKKYKQHQPT DMVMENLKK LLTYCEDVYL YYKLAYEHKF YEIVNVLLKD PQTGCCLKDM LAG

UniProtKB: Spatacsin

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Macromolecule #2: Zinc finger FYVE domain-containing protein 26

MacromoleculeName: Zinc finger FYVE domain-containing protein 26 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 284.943906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNHPFGKEEA ASQKQLFGFF CECLRRGEWE LAQACVPQLQ EGQGDIPKRV EDILQALVVC PNLLRCGQDI NPQRVAWVWL LVLEKWLAR EKKLLPVVFR RKLEFLLLSE DLQGDIPENI LEELYETLTQ GAVGHVPDGN PRRESWTPRL SSEAVSVLWD L LRQSPQPA ...String:
MNHPFGKEEA ASQKQLFGFF CECLRRGEWE LAQACVPQLQ EGQGDIPKRV EDILQALVVC PNLLRCGQDI NPQRVAWVWL LVLEKWLAR EKKLLPVVFR RKLEFLLLSE DLQGDIPENI LEELYETLTQ GAVGHVPDGN PRRESWTPRL SSEAVSVLWD L LRQSPQPA QALLELLLEE DDGTGLCHWP LQNALVDLIR KALRALQGPD SVPPGVVDAI YGALRTLRCP AEPLGVELHL LC EELLEAC RTEGSPLREE RLLSCLLHKA SRGLLSLYGH TYAEKVTEKP PRATASGKVS PDHLDPERAM LALFSNPNPA EAW KVAYFY CLSNNKHFLE QILVTALTLL KEEDFPNLGC LLDREFRPLS CLLVLLGWTH CQSLESAKRL LQTLHRTQGP GCDE LLRDA CDGLWAHLEV LEWCIQQSSN PIPKRDLLYH LHGGDSHSVL YTLHHLTNLP ALREEDVLKL LQKVPAKDPQ QEPDA VDAP VPEHLSQCQN LTLYQGFCAM KYAIYALCVN SHQHSQCQDC KDSLSEDLAS ATEPANDSLS SPGAANLFST YLARCQ QYL CSIPDSLCLE LLENIFSLLL ITSADLHPEP HLPEDYAEDD DIEGKSPSGL RSPSESPQHI AHPERKSERG SLGVPKT LA YTMPSHVKAE PKDSYPGPHR HSFLDLKHFT SGISGFLADE FAIGAFLRLL QEQLDEISSR SPPEKPKQES QSCSGSRD G LQSRLHRLSK VVSEAQWRHK VVTSNHRSEE QPSRRYQPAT RHPSLRRGRR TRRSQADGRD RGSNPSLEST SSELSTSTS EGSLSAMSGR NELHSRLHPH PQSSLIPMMF SPPESLLASC ILRGNFAEAH QVLFTFNLKS SPSSGELMFM ERYQEVIQEL AQVEHKIEN QNSDAGSSTI RRTGSGRSTL QAIGSAAAAG MVFYSISDVT DKLLNTSGDP IPMLQEDFWI STALVEPTAP L REVLEDLS PPAMAAFDLA CSQCQLWKTC KQLLETAERR LNSSLERRGR RIDHVLLNAD GIRGFPVVLQ QISKSLNYLL MS ASQTKSE SVEEKGGGPP RCSITELLQM CWPSLSEDCV ASHTTLSQQL DQVLQSLREA LELPEPRTPP LSSLVEQAAQ KAP EAEAHP VQIQTQLLQK NLGKQTPSGS RQMDYLGTFF SYCSTLAAVL LQSLSSEPDH VEVKVGNPFV LLQQSSSQLV SHLL FERQV PPERLAALLA QENLSLSVPQ VIVSCCCEPL ALCSSRQSQQ TSSLLTRLGT LAQLHASHCL DDLPLSTPSS PRTTE NPTL ERKPYSSPRD SSLPALTSSA LAFLKSRSKL LATVACLGAS PRLKVSKPSL SWKELRGRRE VPLAAEQVAR ECERLL EQF PLFEAFLLAA WEPLRGSLQQ GQSLAVNLCG WASLSTVLLG LHSPIALDVL SEAFEESLVA RDWSRALQLT EVYGRDV DD LSSIKDAVLS CAVACDKEGW QYLFPVKDAS LRSRLALQFV DRWPLESCLE ILAYCISDTA VQEGLKCELQ RKLAELQV Y QKILGLQSPP VWCDWQTLRS CCVEDPSTVM NMILEAQEYE LCEEWGCLYP IPREHLISLH QKHLLHLLER RDHDKALQL LRRIPDPTMC LEVTEQSLDQ HTSLATSHFL ANYLTTHFYG QLTAVRHREI QALYVGSKIL LTLPEQHRAS YSHLSSNPLF MLEQLLMNM KVDWATVAVQ TLQQLLVGQE IGFTMDEVDS LLSRYAEKAL DFPYPQREKR SDSVIHLQEI VHQAADPETL P RSPSAEFS PAAPPGISSI HSPSLRERSF PPTQPSQEFV PPATPPARHQ WVPDETESIC MVCCREHFTM FNRRHHCRRC GR LVCSSCS TKKMVVEGCR ENPARVCDQC YSYCNKDVPE EPSEKPEALD SSKNESPPYS FVVRVPKADE VEWILDLKEE ENE LVRSEF YYEQAPSASL CIAILNLHRD SIACGHQLIE HCCRLSKGLT NPEVDAGLLT DIMKQLLFSA KMMFVKAGQS QDLA LCDSY ISKVDVLNIL VAAAYRHVPS LDQILQPAAV TRLRNQLLEA EYYQLGVEVS TKTGLDTTGA WHAWGMACLK AGNLT AARE KFSRCLKPPF DLNQLNHGSR LVQDVVEYLE STVRPFVSLQ DDDYFATLRE LEATLRTQSL SLAVIPEGKI MNNTYY QEC LFYLHNYSTN LAIISFYVRH SCLREALLHL LNKESPPEVF IEGIFQPSYK SGKLHTLENL LESIDPTLES WGKYLIA AC QHLQKKNYYH ILYELQQFMK DQVRAAMTCI RFFSHKAKSY TELGEKLSWL LKAKDHLKIY LQETSRSSGR KKTTFFRK K MTAADVSRHM NTLQLQMEVT RFLHRCESAG TSQITTLPLP TLFGNNHMKM DVACKVMLGG KNVEDGFGIA FRVLQDFQL DAAMTYCRAA RQLVEKEKYS EIQQLLKCVS ESGMAAKSDG DTILLNCLEA FKRIPPQELE GLIQAIHNDD NKVRAYLICC KLRSAYLIA VKQEHSRATA LVQQVQQAAK SSGDAVVQDI CAQWLLTSHP RGAHGPGSRK

UniProtKB: Zinc finger FYVE domain-containing protein 26

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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

MicroscopeTFS 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: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234969
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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