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- EMDB-54257: Mammalian AP3 complex on tubular membranes (ARF1 centered Beta3-A... -

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Basic information

Entry
Database: EMDB / ID: EMD-54257
TitleMammalian AP3 complex on tubular membranes (ARF1 centered Beta3-ARF1 dimer-Delta interface)
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
    • 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 / clathrin-coated vesicle cargo loading, AP-3-mediated / AP-type membrane coat adaptor complex / AP-3 adaptor complex / anterograde synaptic vesicle transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / platelet dense granule organization / synaptic vesicle recycling / melanosome assembly ...synaptic vesicle coating / clathrin-coated vesicle cargo loading, AP-3-mediated / AP-type membrane coat adaptor complex / AP-3 adaptor complex / anterograde synaptic vesicle transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / platelet dense granule organization / synaptic vesicle recycling / melanosome assembly / Glycosphingolipid transport / clathrin adaptor complex / regulation of receptor internalization / Intra-Golgi traffic / Golgi to vacuole transport / regulation of Arp2/3 complex-mediated actin nucleation / vesicle organization / Synthesis of PIPs at the Golgi membrane / clathrin-coated vesicle membrane / anterograde axonal transport / Nef Mediated CD4 Down-regulation / dendritic spine organization / lysosomal transport / 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 / insulin receptor signaling pathway / presynapse / G protein activity / early endosome / endosome membrane / neuron projection / postsynaptic density / Golgi membrane / protein domain specific binding / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / Golgi apparatus / protein-containing complex / RNA binding / extracellular exosome / 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 / AP-3 complex subunit delta / Adaptor-related protein complex 3, mu 1 subunit / 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: 8.9 Å
AuthorsKaufman JGG / Tagiltsev G / Briggs JAG / Owen DJ
Funding support United Kingdom, European Union, 8 items
OrganizationGrant numberCountry
Wellcome Trust227915/Z/23/Z United Kingdom
Wellcome Trust207455/Z/17/Z United Kingdom
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_54257.png

Downloads & links

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Map

FileDownload / File: emd_54257.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 208 pix.
= 499.2 Å		2.4 Å/pix.
x 208 pix.
= 499.2 Å		2.4 Å/pix.
x 208 pix.
= 499.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
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Contour LevelBy AUTHOR: 0.00696
Minimum - Maximum-0.010710903 - 0.022261957
Average (Standard dev.)0.00004092894 (±0.0015421925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 499.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54257_msk_1.map
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Half map: #1

Fileemd_54257_half_map_1.map
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Half map: #2

Fileemd_54257_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
    • 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Pan troglodytes (chimpanzee)
Molecular weightTheoretical: 74.584289 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHHHHH MASNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL DAMKRIVGMI AKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP I MMLAIKEA ...String:
HHHHHHHHHH MASNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL DAMKRIVGMI AKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP I MMLAIKEA SADLSPYVRK NAAHAIQKLY SLDPEQKEML IEVIEKLLKD KSTLVAGSVV MAFEEVCPDR IDLIHKNYRK LC NLLVDVE EWGQVVIIHM LTRYARTQFV SPWKEGDELE DNGKNFYESD DDQKEKTDKK KKPYTMDPDH RLLIRNTKPL LQS RNAAVV MAVAQLYWHI SPKSEAGIIS KSLVRLLRSN REVQYIVLQN IATMSIQRKG MFEPYLKSFY VRSTDPTMIK TLKL EILTN LANEANISTL LREFQTYVKS QDKQFAAATI QTIGRCATNI LEVTDTCLNG LVCLLSNRDE IVVAESVVVI KKLLQ MQPA QHGEIIKHMA KLLDSITVPV ARASILWLIG ENCERVPKIA PDVLRKMAKS FTSEDDLVKL QILNLGAKLY LTNSKQ TKL LTQYILNLGK YDQNYDIRDR TRFIRQLIVP NEKSGALSKY AKKIFLAQKP APLLESPFKD RDHFQLGTLS HTLNIKA TG YLELSNWPEV APDPSV

UniProtKB: AP-3 complex subunit beta

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Macromolecule #2: AP-3 complex subunit delta

MacromoleculeName: AP-3 complex subunit delta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.628641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD NIAVKANAVC KLTYLQMLGY DISWAAFNII EVMSASKFT FKRIGYLAAS QSFHEGTNVI MLTTNQIRKD LSSPSQYDTG VALTGLSCFV TPDLARDLAN DIMTLMSHTK P YIRKKAVL ...String:
MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD NIAVKANAVC KLTYLQMLGY DISWAAFNII EVMSASKFT FKRIGYLAAS QSFHEGTNVI MLTTNQIRKD LSSPSQYDTG VALTGLSCFV TPDLARDLAN DIMTLMSHTK P YIRKKAVL IMYKVFLKYP ESLRPAFPRL KEKLEDPDPG VQSAAVNVIC ELARRNPKNY LSLAPLFFKL MTSSTNNWVL IK IIKLFGA LTPLEPRLGK KLIEPLTNLI HSTSAMSLLY ECVNTVIAVL ISLSSGMPNH SASIQLCVQK LRILIEDSDQ NLK YLGLLA MSKILKTHPK SVQSHKDLIL QCLDDKDESI RLRALDLLYG MVSKKNLMEI VKKLMTHVDK AEGTTYRDEL LTKI IDICS QSNYQYITNF EWYISILVEL TRLEGTRHGH LIAAQMLDVA IRVKAIRKFA VSQMSALLDS AHLLASSTQR NGICE VLYA AAWICGEFSE HLQEPHHTLE AMLRPRVTTL PGHIQAVYVQ NVVKLYASIL QQKEQAGEAE GAQAVTQLMV DRLPQF VQS ADLEVQERAS CILQLVKHIQ KLQAKDVPVA EEVSALFAGE LNPVAPKAQK KVPVPEGLDL DAWINEPLSD SESEDER PR AVFHEEEQRR PKHRPSEADE EELARRREAR KQEQANNPFY IKSSPSPQKR YQDTPGVEHI PVVQIDLSVP LKVPGLPM S DQYVKLEEER RHRQKLEKDK RRKKRKEKEK KGKRRHSSLP TESDEDIAPA QQVDIVTEEM PENALPSDED DKDPNDPYR ALDIDLDKPL ADSEKLPIQK HRNTETSKSP EKDVPMVEKK SKKPKKKEKK HKEKERDKEK KKEKEKKAED LDFWLSTTPP PAPAPAPAP VPSTDECEDA KTEAQGEEDD AEGQDQDKKS PKPKKKKHRK EKEERTKGKK KSKKQPPGSE EAAGEPVQNG A PEEEQLPP ESSYSLLAEN SYVKMTCDIR GSLQEDSQVT VAIVLENRSS SILKGMELSV LDSLNARMAR PQGSSVHDGV PV PFQLPPG VSNEAQYVFT IQSIVMAQKL KGTLSFIAKN DEGATHEKLD FRLHFSCSSY LITTPCYSDA FAKLLESGDL SMS SIKVDG IRMSFQNLLA KICFHHHFSV VERVDSCASM YSRSIQGHHV CLLVKKGENS VSVDGKCSDS TLLSNLLEEM KATL AKC

UniProtKB: AP-3 complex subunit delta

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Macromolecule #3: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.721742 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGNIFANLFK GLFGKKEMRI LMVGLDAAGK TTILYKLKLG EIVTTIPTIG FNVETVEYKN ISFTVWDVGG QDKIRPLWRH YFQNTQGLI FVVDSNDRER VNEAREELMR MLAEDELRDA VLLVFANKQD LPNAMNAAEI TDKLGLHSLR HRNWYIQATC A TSGDGLYE GLDWLSNQLR NQK

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: 2 / 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.780088 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MIKAILIFNN YGKPRLSKFY QPYSEDTQQQ IIRETFHLVS KRDENVCNFL EGGLLIGGSD NKLIYRHYAT LYFVFCVDSS ESELGILDL IQVFVETLDK CFENVCELDL IFHVDKVHNI LAEMVMGGMV LETNMNEIVT QIDAQNKLEK SEAGLAGAPA R AVSAVKNM ...String:
MIKAILIFNN YGKPRLSKFY QPYSEDTQQQ IIRETFHLVS KRDENVCNFL EGGLLIGGSD NKLIYRHYAT LYFVFCVDSS ESELGILDL IQVFVETLDK CFENVCELDL IFHVDKVHNI LAEMVMGGMV LETNMNEIVT QIDAQNKLEK SEAGLAGAPA R AVSAVKNM NLPEIPRNIN IGDISIKVPN LPSFK

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
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 284 K / Instrument: FEI VITROBOT MARK IV
Detailsurified 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: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 9429
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
DetailsTwo copies of previously modeled C1 coordinates of AP3 bound by ARF1 dimers was rigid body docked into the ARF1 centered reconstruction using UCSF ChimeraX. Duplicate ARF1 dimers were deleted.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9rty:
Mammalian AP3 complex on tubular membranes (ARF1 centered Beta3-ARF1 dimer-Delta interface)

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