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- EMDB-45207: AP-3 bound to myristoylated Arf1 (Q71L) -

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Basic information

Entry
Database: EMDB / ID: EMD-45207
TitleAP-3 bound to myristoylated Arf1 (Q71L)
Map dataB factor sharpened map
Sample
  • Complex: AP-3 bound to myristoylated Arf1 (Q71L)
    • Protein or peptide: AP-3 complex subunit delta-1
    • Protein or peptide: AP-3 complex subunit beta-1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: AP-3 complex subunit sigma-1
    • Protein or peptide: ADP-ribosylation factor 1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsAdaptor Protein complex / AP-3 / Lysosomal transport / Endosomal transport / Protein trafficking / TRANSPORT PROTEIN
Function / homology
Function and homology information


synaptic vesicle coating / synaptic vesicle budding from endosome / establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / zinc ion import into lysosome / AP-type membrane coat adaptor complex / skin epidermis development / synaptic vesicle membrane organization / AP-3 adaptor complex / anterograde synaptic vesicle transport ...synaptic vesicle coating / synaptic vesicle budding from endosome / establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / zinc ion import into lysosome / AP-type membrane coat adaptor complex / skin epidermis development / synaptic vesicle membrane organization / AP-3 adaptor complex / anterograde synaptic vesicle transport / microvesicle / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / presynaptic endosome / Golgi to vacuole transport / synaptic vesicle recycling / postsynaptic recycling endosome / clathrin adaptor complex / platelet dense granule organization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly / granulocyte differentiation / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / postsynaptic neurotransmitter receptor internalization / positive regulation of NK T cell differentiation / GTP-dependent protein binding / neurotransmitter receptor transport, postsynaptic endosome to lysosome / 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 / protein targeting to lysosome / respiratory system process / melanosome organization / anterograde axonal transport / protein localization to membrane / intracellular zinc ion homeostasis / Nef Mediated CD4 Down-regulation / dendritic spine organization / protein localization to cell surface / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / toll-like receptor signaling pathway / Golgi Associated Vesicle Biogenesis / lysosome organization / lung morphogenesis / cell leading edge / Association of TriC/CCT with target proteins during biosynthesis / Synthesis of PIPs at the plasma membrane / homeostasis of number of cells / intracellular copper ion homeostasis / intracellular transport / single fertilization / hematopoietic progenitor cell differentiation / COPI-mediated anterograde transport / vesicle-mediated transport / transport vesicle / axon cytoplasm / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / small monomeric GTPase / intracellular protein transport / mRNA transcription by RNA polymerase II / cytoplasmic vesicle membrane / protein modification process / terminal bouton / cell morphogenesis / cellular response to virus / small GTPase binding / endocytosis / blood coagulation / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / synaptic vesicle / protein phosphatase binding / cytoplasmic vesicle / spermatogenesis / early endosome / lysosome / postsynapse / endosome membrane / postsynaptic density / neuron projection / inflammatory response / protein domain specific binding / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / magnesium ion binding / positive regulation of transcription by RNA polymerase II
Similarity search - Function
AP-3 complex subunit sigma / AP-3 complex subunit delta domain, metazoa / AP-3 complex subunit delta-1 / 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 / Clathrin-adaptor complex-3 beta-1 subunit C-terminal / Adaptor protein complex AP-3, delta subunit ...AP-3 complex subunit sigma / AP-3 complex subunit delta domain, metazoa / AP-3 complex subunit delta-1 / 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 / 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 / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Small GTPase superfamily, ARF type / small GTPase Arf family 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-1 / AP-3 complex subunit delta-1 / ADP-ribosylation factor 1 / AP-3 complex subunit sigma-1 / AP-3 complex subunit mu-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsBegley MC / Baker RW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM150960 United States
CitationJournal: To Be Published
Title: A structure-based mechanism for initiation of AP-3 coated vesicle formation
Authors: Begley M / Baker RW
History
DepositionJun 6, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45207.png

Downloads & links

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Map

FileDownload / File: emd_45207.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.504133 - 1.1040016
Average (Standard dev.)0.0003716363 (±0.019176668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45207_msk_1.map
Projections & Slices
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Mask #2

Fileemd_45207_msk_2.map
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Mask #3

Fileemd_45207_msk_3.map
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Additional map: Locres file

Fileemd_45207_additional_1.map
AnnotationLocres file
Projections & Slices
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Additional map: deepEMhancer sharpened map

Fileemd_45207_additional_2.map
AnnotationdeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Full, unsharpened mask

Fileemd_45207_additional_3.map
AnnotationFull, unsharpened mask
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half map 2

Fileemd_45207_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map 1

Fileemd_45207_half_map_2.map
AnnotationHalf map 1
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Sample components

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Entire : AP-3 bound to myristoylated Arf1 (Q71L)

EntireName: AP-3 bound to myristoylated Arf1 (Q71L)
Components
  • Complex: AP-3 bound to myristoylated Arf1 (Q71L)
    • Protein or peptide: AP-3 complex subunit delta-1
    • Protein or peptide: AP-3 complex subunit beta-1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: AP-3 complex subunit sigma-1
    • Protein or peptide: ADP-ribosylation factor 1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: AP-3 bound to myristoylated Arf1 (Q71L)

SupramoleculeName: AP-3 bound to myristoylated Arf1 (Q71L) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 240 KDa

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

MacromoleculeName: AP-3 complex subunit delta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.381977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD NIAVKANAVC KLTYLQMLGY DISWAAFNII EVMSASKFT FKRIGYLAAS QSFHEGTDVI MLTTNQIRKD LSSPSQYDTG VALTGLSCFV TPDLARDLAN DIMTLMSHTK P YIRKKAVL ...String:
MALKMVKGSI DRMFDKNLQD LVRGIRNHKE DEAKYISQCI DEIKQELKQD NIAVKANAVC KLTYLQMLGY DISWAAFNII EVMSASKFT FKRIGYLAAS QSFHEGTDVI 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 KVPV

UniProtKB: AP-3 complex subunit delta-1

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

MacromoleculeName: AP-3 complex subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.499609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL DAMKRIVGMI AKGKNASELF PAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS A DLSPYVRK ...String:
MSSNSFPYNE QSGGGEATEL GQEATSTISP SGAFGLFSSD LKKNEDLKQM LESNKDSAKL DAMKRIVGMI AKGKNASELF PAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPNQ LIRASALRVL SSIRVPIIVP IMMLAIKEAS A DLSPYVRK NAAHAIQKLY SLDPEQKEML IEVIEKLLKD KSTLVAGSVV MAFEEVCPDR IDLIHKNYRK LCNLLVDVEE WG QVVIIHM LTRYARTQFV SPWKEGDELE DNGKNFYESD DDQKEKTDKK KKPYTMDPDH RLLIRNTKPL LQSRNAAVVM AVA QLYWHI SPKSEAGIIS KSLVRLLRSN REVQYIVLQN IATMSIQRKG MFEPYLKSFY VRSTDPTMIK TLKLEILTNL ANEA NISTL LREFQTYVKS QDKQFAAATI QTIGRCATNI LEVTDTCLNG LVCLLSNRDE IVVAESVVVI KKLLQMQPAQ HGEII KHMA KLLDSITVPV ARASILWLIG ENCERVPKIA PDVLRKMAKS FTSEDDLVKL QILNLGAKLY LTNSKQTKLL TQYILN LGK YDQNYDIRDR TRFIRQLIVP NVKSGALSKY AKKIFLAQKP APLLESPFKD RDHFQLGTLS HTLNIKATGY LELSNWP EV APDPSVRNVE VIELAKEWTP AGKAKQENSA KKFYS

UniProtKB: AP-3 complex subunit beta-1

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

MacromoleculeName: AP-3 complex subunit mu-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.989965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIHSLFLINC SGDIFLEKHW KSVVSQSVCD YFFEAQEKAA DVENVPPVIS TPHHYLISIY RDKLFFVSVI QTEVPPLFVI EFLHRVADT FQDYFGECSE AAIKDNVVIV YELLEEMLDN GFPLATESNI LKELIKPPTI LRSVVNSITG SSNVGDTLPT G QLSNIPWR ...String:
MIHSLFLINC SGDIFLEKHW KSVVSQSVCD YFFEAQEKAA DVENVPPVIS TPHHYLISIY RDKLFFVSVI QTEVPPLFVI EFLHRVADT FQDYFGECSE AAIKDNVVIV YELLEEMLDN GFPLATESNI LKELIKPPTI LRSVVNSITG SSNVGDTLPT G QLSNIPWR RAGVKYTNNE AYFDVVEEID AIIDKSGSTV FAEIQGVIDA CIKLSGMPDL SLSFMNPRLL DDVSFHPCIR FK RWESERV LSFIPPDGNF RLISYRVSSQ NLVAIPVYVK HSISFKENSS CGRFDITIGP KQNMGKTIEG ITVTVHMPKV VLN MNLTPT QGSYTFDPVT KVLTWDVGKI TPQKLPSLKG LVNLQSGAPK PEENPSLNIQ FKIQQLAISG LKVNRLDMYG EKYK PFKGV KYVTKAGKFQ VRT

UniProtKB: AP-3 complex subunit mu-1

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

MacromoleculeName: AP-3 complex subunit sigma-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.755061 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKAILIFNN HGKPRLSKFY QPYSEDTQQQ IIRETFHLVS KRDENVCNFL EGGLLIGGSD NKLIYRHYAT LYFVFCVDSS ESELGILDL IQVFVETLDK CFENVCELDL IFHVDKVHNI LAEMVMGGMV LETNMNEIVT QIDAQNKLEK SEAGLAGAPA R AVSAVKNM ...String:
MIKAILIFNN HGKPRLSKFY 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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Macromolecule #5: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.775812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GNIFANLFKG LFGKKEMRIL MVGLDAAGKT TILYKLKLGE IVTTIPTIGF NVETVEYKNI SFTVWDVGGL DKIRPLWRHY FQNTQGLIF VVDSNDRERV NEAREELMRM LAEDELRDAV LLVFANKQDL PNAMNAAEIT DKLGLHSLRH RNWYIQATCA T SGDGLYEG LDWLSNQLRN QKSL

UniProtKB: ADP-ribosylation factor 1

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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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

Concentration1.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4Sodium Phosphate (Dibasic)
1.8 mMKH2PO4Potassium Phosphate (Monobasic)
300.0 mMNaClSodium Chloride
1.0 mMC9H15O6PTCEP

Details: 1x PBS (pH 7.4), 300mM NaCl, 1mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
Details: Used Quantifoil Active grids - backside gold coated before plasma cleaning. 12 mA used for plasma cleaning.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: SPOTITON / Details: Commercialized version - Chameleon.
DetailsSpecimen appeared as a monodisperse peak via size exclusion chromatography (SEC)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.97 e/Å2
Details: 4 datasets collected, processed independently, and merged.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 81000
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

Particle selectionDetails: Mixture of blob picker, template picker, crYOLO, and Topaz
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Details: NU refinement in cryoSPARC / Number images used: 285082
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9c58:
AP-3 bound to myristoylated Arf1 (Q71L)

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