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- EMDB-54255: Mammalian AP3 complex on tubular membranes (AP3 centered) -

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Basic information

Entry
Database: EMDB / ID: EMD-54255
TitleMammalian AP3 complex on tubular membranes (AP3 centered)
Map data
Sample
  • Complex: Mammalian AP-3 complex assembled on tubular membranes
    • Protein or peptide: AP-3 complex subunit beta
    • Protein or peptide: AP-3 complex subunit delta-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: AP-3 complex subunit sigma-1
KeywordsCargo adapter / Coat / trafficking / ENDOCYTOSIS
Function / homology
Function and homology information


synaptic vesicle coating / synaptic vesicle membrane organization / clathrin-coated vesicle cargo loading, AP-3-mediated / zinc ion import into lysosome / AP-type membrane coat adaptor complex / AP-3 adaptor complex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / anterograde synaptic vesicle transport / synaptic vesicle budding from endosome / endosome to melanosome transport ...synaptic vesicle coating / synaptic vesicle membrane organization / clathrin-coated vesicle cargo loading, AP-3-mediated / zinc ion import into lysosome / AP-type membrane coat adaptor complex / AP-3 adaptor complex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / anterograde synaptic vesicle transport / synaptic vesicle budding from endosome / endosome to melanosome transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / platelet dense granule organization / synaptic vesicle recycling / melanosome assembly / Glycosphingolipid transport / clathrin adaptor complex / presynaptic endosome / regulation of receptor internalization / Intra-Golgi traffic / Golgi to vacuole transport / positive regulation of NK T cell differentiation / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / clathrin-coated vesicle membrane / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / protein targeting to vacuole / melanosome organization / anterograde axonal transport / Nef Mediated CD4 Down-regulation / dendritic spine organization / protein localization to membrane / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Synthesis of PIPs at the plasma membrane / cell leading edge / intracellular copper ion homeostasis / transport vesicle / COPI-mediated anterograde transport / vesicle-mediated transport / axon cytoplasm / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoplasmic vesicle membrane / small monomeric GTPase / sarcomere / intracellular protein transport / cellular response to virus / terminal bouton / insulin receptor signaling pathway / presynapse / G protein activity / early endosome / endosome membrane / neuron projection / postsynaptic density / postsynapse / Golgi membrane / protein domain specific binding / lysosomal membrane / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / magnesium ion binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
AP-3 complex subunit sigma / AP-3 complex subunit delta domain, metazoa / : / AP-3 complex subunit delta-1 / AP3 Mu C-terminal domain / Bovine leukaemia virus receptor (BLVR) / AP-3 complex subunit beta, C-terminal domain / AP-3 complex subunit beta 1, serine-rich domain / : / Clathrin-adaptor complex-3 beta-1 subunit C-terminal ...AP-3 complex subunit sigma / AP-3 complex subunit delta domain, metazoa / : / AP-3 complex subunit delta-1 / AP3 Mu C-terminal domain / Bovine leukaemia virus receptor (BLVR) / AP-3 complex subunit beta, C-terminal domain / AP-3 complex subunit beta 1, serine-rich domain / : / Clathrin-adaptor complex-3 beta-1 subunit C-terminal / Serine-rich region of AP3B1, clathrin-adaptor complex / AP-3 complex subunit beta-1, C-terminal domain / Clathrin-adaptor complex-3 beta-1 subunit C-terminal / Adaptor protein complex AP-3, delta subunit / AP-3 complex subunit beta / Adaptor protein complex, sigma subunit / ADP-ribosylation factor 1-5 / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / AP complex subunit beta / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / AP-2 complex subunit mu, C-terminal superfamily / Adaptin N terminal region / Small GTPase superfamily, ARF type / Mu homology domain / Mu homology domain (MHD) profile. / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AP-3 complex subunit beta / Adaptor-related protein complex 3, mu 1 subunit / AP-3 complex subunit delta-1 / ADP-ribosylation factor 1 / AP-3 complex subunit sigma-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Pan troglodytes (chimpanzee) / Rattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 7.4 Å
AuthorsKaufman JGG / Tagiltsev G / Briggs JAG / Owen DJ
Funding support United Kingdom, Germany, European Union, 9 items
OrganizationGrant numberCountry
Wellcome Trust227915/Z/23/Z United Kingdom
Wellcome Trust207455/Z/17/Z United Kingdom
Max Planck Society Germany
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N013433/1 United Kingdom
European Molecular Biology Organization (EMBO)ALTF-383-2022European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W005905/ United Kingdom
UK Research and Innovation (UKRI)UKRI715 United Kingdom
Wellcome Trust210481 United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Architecture of clathrin-independent AP3:ARF1-coated carriers.
Authors: Jonathan G G Kaufman / Grigory Tagiltsev / Danièle S Stalder / Rebecca J Taylor / Ioana Sava / Hui Guo / Katarzyna A Ciazynska / Nathan R Zaccai / Sally R Gray / Yvonne Vallis / Stefan ...Authors: Jonathan G G Kaufman / Grigory Tagiltsev / Danièle S Stalder / Rebecca J Taylor / Ioana Sava / Hui Guo / Katarzyna A Ciazynska / Nathan R Zaccai / Sally R Gray / Yvonne Vallis / Stefan Höning / Bernard T Kelly / David C Gershlick / John A G Briggs / David J Owen /
Abstract: The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. AP3 is generally believed to localize to clathrin-free, ARF1- ...The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. AP3 is generally believed to localize to clathrin-free, ARF1-positive, elongated carriers in cells, but the architecture of AP3-based coats was unknown. Using in vitro reconstitution and cryo-electron tomography, we demonstrate that AP3:ARF1 spontaneously remodels membranes containing cargo and the phosphoinositide PI(3,5)P into tubular structures coated in spiraling rows of AP3 arches and ARF1 dimers. Targeted point mutations disrupting critical AP3:ARF1 and AP3:AP3 lattice interfaces disrupt AP3 recruitment, carrier formation, and lysosomal cargo trafficking in cells. We propose that AP3 generates tubular carriers on endosomes by organizing ARF1 dimers into elongated membrane-deforming arrays while simultaneously selecting cargo. By demonstrating that AP3:ARF1 can generate carriers without using a clathrin lattice, we explain the clathrin independence of AP3-mediated trafficking.
History
DepositionJul 3, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54255.png

Downloads & links

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Map

FileDownload / File: emd_54255.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 182 pix.
= 400.4 Å		2.2 Å/pix.
x 182 pix.
= 400.4 Å		2.2 Å/pix.
x 182 pix.
= 400.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.007814548 - 0.01318146
Average (Standard dev.)0.00005880319 (±0.0005775094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions182182182
Spacing182182182
CellA=B=C: 400.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54255_msk_1.map
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Half map: #2

Fileemd_54255_half_map_1.map
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Half map: #1

Fileemd_54255_half_map_2.map
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Sample components

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Entire : Mammalian AP-3 complex assembled on tubular membranes

EntireName: Mammalian AP-3 complex assembled on tubular membranes
Components
  • Complex: Mammalian AP-3 complex assembled on tubular membranes
    • Protein or peptide: AP-3 complex subunit beta
    • Protein or peptide: AP-3 complex subunit delta-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: AP-3 complex subunit sigma-1

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Supramolecule #1: Mammalian AP-3 complex assembled on tubular membranes

SupramoleculeName: Mammalian AP-3 complex assembled on tubular membranes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: helical
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1592.786 kDa/nm

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Macromolecule #1: AP-3 complex subunit beta

MacromoleculeName: AP-3 complex subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pan troglodytes (chimpanzee)
Molecular weightTheoretical: 63.956988 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KNEDLKQMLE SNKDSAKLDA MKRIVGMIAK GKNASELFPA VVKNVASKNI EIKKLVYVYL VRYAEEQQDL ALLSISTFQR ALKDPNQLI RASALRVLSS IRVPIIVPIM MLAIKEASAD LSPYVRKNAA HAIQKLYSLD PEQKEMLIEV IEKLLKDKST L VAGSVVMA ...String:
KNEDLKQMLE SNKDSAKLDA MKRIVGMIAK GKNASELFPA VVKNVASKNI EIKKLVYVYL VRYAEEQQDL ALLSISTFQR ALKDPNQLI RASALRVLSS IRVPIIVPIM MLAIKEASAD LSPYVRKNAA HAIQKLYSLD PEQKEMLIEV IEKLLKDKST L VAGSVVMA FEEVCPDRID LIHKNYRKLC NLLVDVEEWG QVVIIHMLTR YARTQFVSPW TMDPDHRLLI RNTKPLLQSR NA AVVMAVA QLYWHISPKS EAGIISKSLV RLLRSNREVQ YIVLQNIATM SIQRKGMFEP YLKSFYVRST DPTMIKTLKL EIL TNLANE ANISTLLREF QTYVKSQDKQ FAAATIQTIG RCATNILEVT DTCLNGLVCL LSNRDEIVVA ESVVVIKKLL QMQP AQHGE IIKHMAKLLD SITVPVARAS ILWLIGENCE RVPKIAPDVL RKMAKSFTSE DDLVKLQILN LGAKLYLTNS KQTKL LTQY ILNLGKYDQN YDIRDRTRFI RQLIVPNEKS GALSKYAKKI FLAQKPAPLL ESPFKDRDHF QLGTLSHTLN IKATGY LEL

UniProtKB: AP-3 complex subunit beta

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Macromolecule #2: AP-3 complex subunit delta-1

MacromoleculeName: AP-3 complex subunit delta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.061336 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LQDLVRGIRN HKEDEAKYIS QCIDEIKQEL KQDNIAVKAN AVCKLTYLQM LGYDISWAAF NIIEVMSASK FTFKRIGYLA ASQSFHEGT NVIMLTTNQI RKDLSSPSQY DTGVALTGLS CFVTPDLARD LANDIMTLMS HTKPYIRKKA VLIMYKVFLK Y PESLRPAF ...String:
LQDLVRGIRN HKEDEAKYIS QCIDEIKQEL KQDNIAVKAN AVCKLTYLQM LGYDISWAAF NIIEVMSASK FTFKRIGYLA ASQSFHEGT NVIMLTTNQI RKDLSSPSQY DTGVALTGLS CFVTPDLARD LANDIMTLMS HTKPYIRKKA VLIMYKVFLK Y PESLRPAF PRLKEKLEDP DPGVQSAAVN VICELARRNP KNYLSLAPLF FKLMTSSTNN WVLIKIIKLF GALTPLEPRL GK KLIEPLT NLIHSTSAMS LLYECVNTVI AVLISLSSGM PNHSASIQLC VQKLRILIED SDQNLKYLGL LAMSKILKTH PKS VQSHKD LILQCLDDKD ESIRLRALDL LYGMVSKKNL MEIVKKLMTH VDKAEGTTYR DELLTKIIDI CSQSNYQYIT NFEW YISIL VELTRLEGTR HGHLIAAQML DVAIRVKAIR KFAVSQMSAL LDSAHLLASS TQRNGICEVL YAAAWICGEF SEHLQ EPHH TLEAMLRPRV TTLPGHIQAV YVQNVVKLYA SILQQKEQAG EAEGAQAVTQ LMVDRLPQFV QSADLEVQER ASCILQ LVK HIQKLQAKDV PVAEEVSALF AGELNPVAPK AQKKVPVPEG LDLDAWINEP LS

UniProtKB: AP-3 complex subunit delta-1

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Macromolecule #3: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.20993 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
KKEMRILMVG LDAAGKTTIL YKLKLGEIVT TIPTIGFNVE TVEYKNISFT VWDVGGQDKI RPLWRHYFQN TQGLIFVVDS NDRERVNEA REELMRMLAE DELRDAVLLV FANKQDLPNA MNAAEITDKL GLHSLRHRNW YIQATCATSG DGLYEGLDWL S NQLRNQK

UniProtKB: ADP-ribosylation factor 1

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Macromolecule #4: AP-3 complex subunit mu-1

MacromoleculeName: AP-3 complex subunit mu-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 47.01798 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MIHSLFLINC SGDIFLEKHW KSVVSQSVCD YFFEAQEKAA DVENVPPVIS TPHHYLISIY RDKLFFVSVI QTEVSPLFVI EFLHRVADT FQDYFGECSE AAIKDNVVIV YELLEEMLDN GFPLATESNI LKELIKPPTI LRSVVNSITG SSNVGDTLPT G QLSNIPWR ...String:
MIHSLFLINC SGDIFLEKHW KSVVSQSVCD YFFEAQEKAA DVENVPPVIS TPHHYLISIY RDKLFFVSVI QTEVSPLFVI EFLHRVADT FQDYFGECSE AAIKDNVVIV YELLEEMLDN GFPLATESNI LKELIKPPTI LRSVVNSITG SSNVGDTLPT G QLSNIPWR RAGVKYTNNE AYFDVVEEID AIIDKSGSTV FAEIQGVIDA CIKLSGMPDL SLSFMNPRLL DDVSFHPCIR FK RWESERV LSFIPPDGNF RLISYRVSSQ NLVAIPVYVK HNISFKENSS CGRFDITIGP KQNMGKTIEG ITVTVHMPKV VLN MNLTPT QGSYTFDPVT KVLAWDVGKI TPQKLPSLKG LVNLQSGAPK PEENPNLNIQ FKIQQLAISG LKVNRLDMYG EKYK PFKGV KYITKAGKFQ VRT

UniProtKB: Adaptor-related protein complex 3, mu 1 subunit

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

MacromoleculeName: AP-3 complex subunit sigma-1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.566105 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MIKAILIFNN YGKPRLSKFY QPYSEDTQQQ IIRETFHLVS KRDENVCNFL EGGLLIGGSD NKLIYRHYAT LYFVFCVDSS ESELGILDL IQVFVETLDK CFENVCELDL IFHVDKVHNI LAEMVMGGMV LETNMNEIVT QIDAQNKLEK SEAG

UniProtKB: AP-3 complex subunit sigma-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMTris-HClTris(hydroxymethyl)aminomethane-HCl
1.0 mMTCEPTris(2-carboxyethyl)phosphine
GridModel: C-flat-2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 284 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified recombinant AP3 complex was reconstituted with mystoylated ARF1 GTPase on GUV containing lipidated cargo motif sequences (TGN38:CKVTRRPKASDYQRL and MFSD12:GEHTPLLAPATC). Reconstituted AP3 spontaneously assembled to tubulate membranes.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 1 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 42469
ExtractionNumber tomograms: 32 / Number images used: 121939 / Reference model: reference free STA / Software: (Name: UCSF Chimera, subTOM, Warp, M, RELION)
CTF correctionSoftware - Name: Warp / Details: 3DCTF in WARP / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsAlphafold 3 (AF3), was used to generate 5 models of mammalian AP3 in complex with two copies of ARF1 in the GTP bound conformation. As the structure from STA was in a much more extended conformation than AF3 models or previous structures, direct rigid body docking of the complete AF3 model into the STA density was not possible. To create the C1 model the predicted complex was separated into three submodels, each of which was independently fitted into the map as a rigid body. Submodel 1 consisted of sigma3 (1-193), delta (1-387), delta-ARF1 (1-181). Submodel 2 consisted of mu3 (1-418), beta3 (1-472), beta3-ARF1. Submodel 3 consisted of beta3 (473-636) and delta (388-638) formed submodel 3. Rigid body fitting was performed using ChimeraX. This positioned truncated regions of submodels 1 and 2 in close proximity to their adjoining regions in submodel3, thus the split beta3 and delta chains were rejoined into single chains before real-space refinement in COOT to correct bond angles, distances and torsions. Using the previously resolved ARF1 dimer (PDBID: 9C5A), ARF1 was first superimposed with the existing ARF1 on beta3 and delta before rigid docking into the EM density. Flexible regions not accounted for sufficiently by modellable density were removed, these regions are listed as follows; beta3 (1-42), beta3 (259-292), delta (1-17), sigma3 (154-193) and ARF1 (1-13). Side chains and rotamers were not modelled and were therefore removed in ChimeraX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9rtw:
Mammalian AP3 complex on tubular membranes (AP3 centered)

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