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- EMDB-45209: AP-3 Arf1 dimeric interface, focused refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-45209
TitleAP-3 Arf1 dimeric interface, focused refinement
Map datadeepEMHancer sharpened map for Arf1 dimer
Sample
  • Complex: AP-3 Arf1 dimeric interface, focused refinement
    • Protein or peptide: AP-3 complex subunit beta-1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: Lysosome-associated membrane glycoprotein 1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsAdaptor Protein complex / Endosomal Trafficking / Lysosomal Trafficking / Protein transport / AP complex / TRANSPORT PROTEIN
Function / homology
Function and homology information


establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / skin epidermis development / regulation of organelle transport along microtubule / AP-3 adaptor complex / positive regulation of natural killer cell degranulation / granzyme-mediated programmed cell death signaling pathway / anterograde synaptic vesicle transport / microvesicle / phagolysosome membrane ...establishment of protein localization to mitochondrial membrane involved in mitochondrial fission / clathrin-coated vesicle cargo loading, AP-3-mediated / skin epidermis development / regulation of organelle transport along microtubule / AP-3 adaptor complex / positive regulation of natural killer cell degranulation / granzyme-mediated programmed cell death signaling pathway / anterograde synaptic vesicle transport / microvesicle / phagolysosome membrane / Golgi to lysosome transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / establishment of protein localization to organelle / cytolytic granule membrane / postsynaptic recycling endosome / clathrin adaptor complex / platelet dense granule organization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly / granulocyte differentiation / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / postsynaptic neurotransmitter receptor internalization / GTP-dependent protein binding / positive regulation of NK T cell differentiation / Synthesis of PIPs at the Golgi membrane / clathrin-coated vesicle membrane / lysosomal lumen acidification / positive regulation of natural killer cell mediated cytotoxicity / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / respiratory system process / protein targeting to lysosome / melanosome organization / anterograde axonal transport / Nef Mediated CD4 Down-regulation / intracellular zinc ion homeostasis / dendritic spine organization / protein localization to cell surface / long-term synaptic depression / azurophil granule membrane / lysosome organization / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / toll-like receptor signaling pathway / ion channel inhibitor activity / Golgi Associated Vesicle Biogenesis / cell leading edge / lung morphogenesis / Association of TriC/CCT with target proteins during biosynthesis / Synthesis of PIPs at the plasma membrane / autolysosome / autophagosome membrane / ficolin-1-rich granule membrane / homeostasis of number of cells / intracellular copper ion homeostasis / single fertilization / intracellular transport / hematopoietic progenitor cell differentiation / COPI-mediated anterograde transport / vesicle-mediated transport / axon cytoplasm / cytoplasmic vesicle membrane / multivesicular body / 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 / sarcolemma / protein modification process / cell morphogenesis / small GTPase binding / cellular response to virus / endocytosis / blood coagulation / Signaling by BRAF and RAF1 fusions / late endosome membrane / late endosome / synaptic vesicle / melanosome / virus receptor activity / cytoplasmic vesicle / protein phosphatase binding / spermatogenesis / lysosome / early endosome / protein stabilization / postsynaptic density / endosome membrane / neuron projection / inflammatory response / protein domain specific binding / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / GTPase activity
Similarity search - Function
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 / Lysosome-associated membrane glycoprotein, conserved site / AP-3 complex subunit beta / : / Lysosome-associated membrane glycoprotein 2, transmembrane segment / Lysosome-associated membrane glycoproteins duplicated domain signature. ...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 / Lysosome-associated membrane glycoprotein, conserved site / AP-3 complex subunit beta / : / Lysosome-associated membrane glycoprotein 2, transmembrane segment / Lysosome-associated membrane glycoproteins duplicated domain signature. / LAMP glycoproteins transmembrane and cytoplasmic domain signature. / Lysosome-associated membrane glycoprotein / : / Lysosome-associated membrane glycoprotein 2-like, luminal domains / Lysosome-associated membrane glycoprotein family profile. / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / ADP-ribosylation factor 1-5 / 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 / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Mu homology domain / Mu homology domain (MHD) profile. / 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 / Lysosome-associated membrane glycoprotein 1 / ADP-ribosylation factor 1 / AP-3 complex subunit mu-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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: Proc Natl Acad Sci U S A / Year: 2024
Title: A structure-based mechanism for initiation of AP-3 coated vesicle formation.
Authors: Matthew Begley / Mahira Aragon / Richard W Baker /
Abstract: Adaptor protein complex-3 (AP-3) mediates cargo sorting from endosomes to lysosomes and lysosome-related organelles. Recently, it was shown that AP-3 adopts a constitutively open conformation ...Adaptor protein complex-3 (AP-3) mediates cargo sorting from endosomes to lysosomes and lysosome-related organelles. Recently, it was shown that AP-3 adopts a constitutively open conformation compared to the related AP-1 and AP-2 coat complexes, which are inactive until undergoing large conformational changes upon membrane recruitment. How AP-3 is regulated is therefore an open question. To understand the mechanism of AP-3 membrane recruitment and activation, we reconstituted human AP-3 and determined multiple structures in the soluble and membrane-bound states using electron cryo-microscopy. Similar to yeast AP-3, human AP-3 is in a constitutively open conformation. To reconstitute AP-3 activation by adenosine di-phosphate (ADP)-ribosylation factor 1 (Arf1), a small guanosine tri-phosphate (GTP)ase, we used lipid nanodiscs to build Arf1-AP-3 complexes on membranes and determined three structures showing the stepwise conformational changes required for formation of AP-3 coated vesicles. First, membrane recruitment is driven by one of two predicted Arf1 binding sites, which flexibly tethers AP-3 to the membrane. Second, cargo binding causes AP-3 to adopt a fixed position and rigidifies the complex, which stabilizes binding for a second Arf1 molecule. Finally, binding of the second Arf1 molecule provides the template for AP-3 dimerization, providing a glimpse into the first step of coat polymerization. We propose coat polymerization only occurs after cargo engagement, thereby linking cargo sorting with assembly of higher-order coat structures. Additionally, we provide evidence for two amphipathic helices in AP-3, suggesting that AP-3 contributes to membrane deformation during coat assembly. In total, these data provide evidence for the first stages of AP-3-mediated vesicle coat assembly.
History
DepositionJun 6, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45209.png

Downloads & links

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Map

FileDownload / File: emd_45209.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMHancer sharpened map for Arf1 dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å		1.06 Å/pix.
x 400 pix.
= 423.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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-0.0017204892 - 2.0888836
Average (Standard dev.)0.0008835663 (±0.021501599)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45209_msk_1.map
Projections & Slices
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Mask #2

Fileemd_45209_msk_2.map
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Additional map: Unsharpened map for Arf1 dimer

Fileemd_45209_additional_1.map
AnnotationUnsharpened map for Arf1 dimer
Projections & Slices
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Additional map: Sharpened map for Arf1 dimer

Fileemd_45209_additional_2.map
AnnotationSharpened map for Arf1 dimer
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Additional map: Mask for Arf1 dimer

Fileemd_45209_additional_3.map
AnnotationMask for Arf1 dimer
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Additional map: Refined mask for Arf1 dimer

Fileemd_45209_additional_4.map
AnnotationRefined mask for Arf1 dimer
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Additional map: Sharpened map for Arf1 dimer

Fileemd_45209_additional_5.map
AnnotationSharpened map for Arf1 dimer
Projections & Slices
AxesZYX

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Additional map: Map for filtering by local resoluion for Arf1 dimer

Fileemd_45209_additional_6.map
AnnotationMap for filtering by local resoluion for Arf1 dimer
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Half map: Unfiltered half map for Arf1 dimer

Fileemd_45209_half_map_1.map
AnnotationUnfiltered half map for Arf1 dimer
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Half map: Unfiltered half map for Arf1 dimer

Fileemd_45209_half_map_2.map
AnnotationUnfiltered half map for Arf1 dimer
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Sample components

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Entire : AP-3 Arf1 dimeric interface, focused refinement

EntireName: AP-3 Arf1 dimeric interface, focused refinement
Components
  • Complex: AP-3 Arf1 dimeric interface, focused refinement
    • Protein or peptide: AP-3 complex subunit beta-1
    • Protein or peptide: AP-3 complex subunit mu-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: Lysosome-associated membrane glycoprotein 1
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: AP-3 Arf1 dimeric interface, focused refinement

SupramoleculeName: AP-3 Arf1 dimeric interface, focused refinement / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 256 KDa

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

MacromoleculeName: AP-3 complex subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.286523 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 KKFYSGLEVL FQ

UniProtKB: AP-3 complex subunit beta-1

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

MacromoleculeName: AP-3 complex subunit mu-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.775812 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
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 #4: Lysosome-associated membrane glycoprotein 1

MacromoleculeName: Lysosome-associated membrane glycoprotein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.377553 KDa
SequenceString:
GRKRSHAGYQ TI

UniProtKB: Lysosome-associated membrane glycoprotein 1

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / 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 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
2.7 mMKClPotassium Chloride
10.0 mMNa2HPO4Sodium Phosphate (Dibasic)
1.8 mMKH2PO4Potassium Phosphate (Monobasic)
150.0 mMNaClSodium Chloride
1.0 mMC9H15O6PTCEP
5.0 mMC10H16N2O8EDTA
10.0 mMMgCl2Magnesium Chloride
2.0 mMC10H16N5O14P3GTP

Details: 1x PBS (pH 7.4), 150mM NaCl, 1mM TCEP, 2mM GTP, 5mM EDTA, 10mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 200 sec. / Pretreatment - Atmosphere: AIR
Details: Quantifoil Active grids (SPT Labtech) with backside gold coated. Plasma was 12mA for cleaning
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: SPOTITON / Details: Commercial form of the chameleon (SPT Labtech).
DetailsAP-3 dimer bound to myristoylated Arf1 (Q71L) and LAMP1 on a lipid nanodisc; focused refinement on Arf1 dimeric interface

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.37 e/Å2
Details: 2 datasets collected independently and merged for processing
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 122155
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / 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
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9c5a:
AP-3 Arf1 dimeric interface, focused refinement

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