[English] 日本語
Yorodumi
- EMDB-45214: Structure of Human Adaptor Protein Complex AP-3 in the Apo State -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45214
TitleStructure of Human Adaptor Protein Complex AP-3 in the Apo State
Map datadeepEMHancer map of human AP-3 in the Apo state
Sample
  • Complex: Human Adaptor Protein Complex AP-3 in the Apo state
    • 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
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 / skin epidermis development / AP-type membrane coat adaptor complex / synaptic vesicle membrane organization / zinc ion import into lysosome / AP-3 adaptor complex / neurotransmitter receptor transport, postsynaptic endosome to lysosome ...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 / skin epidermis development / AP-type membrane coat adaptor complex / synaptic vesicle membrane organization / zinc ion import into lysosome / AP-3 adaptor complex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / anterograde synaptic vesicle transport / microvesicle / endosome to melanosome transport / Golgi to vacuole transport / synaptic vesicle recycling / postsynaptic recycling endosome / presynaptic endosome / clathrin adaptor complex / platelet dense granule organization / melanosome assembly / granulocyte differentiation / postsynaptic neurotransmitter receptor internalization / GTP-dependent protein binding / positive regulation of NK T cell differentiation / clathrin-coated vesicle membrane / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / protein targeting to vacuole / protein targeting to lysosome / melanosome organization / respiratory system process / anterograde axonal transport / intracellular zinc ion homeostasis / protein localization to membrane / protein localization to cell surface / lysosome organization / toll-like receptor signaling pathway / Golgi Associated Vesicle Biogenesis / lung morphogenesis / Association of TriC/CCT with target proteins during biosynthesis / homeostasis of number of cells / single fertilization / intracellular transport / hematopoietic progenitor cell differentiation / transport vesicle / vesicle-mediated transport / axon cytoplasm / cytoplasmic vesicle membrane / intracellular protein transport / mRNA transcription by RNA polymerase II / terminal bouton / cell morphogenesis / protein modification process / small GTPase binding / endocytosis / blood coagulation / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / presynapse / cytoplasmic vesicle / protein phosphatase binding / spermatogenesis / early endosome / lysosome / postsynapse / endosome membrane / inflammatory response / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / positive regulation of transcription by RNA polymerase II / mitochondrion / membrane
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 / AP-3 complex subunit beta-1, C-terminal domain ...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 / 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 / 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. / : / 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. / Longin-like domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
AP-3 complex subunit beta-1 / AP-3 complex subunit delta-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: 3.6 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

-
Structure visualization

Supplemental images

emd_45214.png

Downloads & links

-
Map

FileDownload / File: emd_45214.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMHancer map of human AP-3 in the Apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0016801807 - 2.1645036
Average (Standard dev.)0.0011362912 (±0.025303898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_45214_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_45214_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map filter by local resolution for human AP-3 in the Apo state

Fileemd_45214_additional_1.map
AnnotationMap filter by local resolution for human AP-3 in the Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map for coloring by local resolution

Fileemd_45214_additional_2.map
AnnotationMap for coloring by local resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: B-factor sharpened map of human AP-3 in the Apo state

Fileemd_45214_additional_3.map
AnnotationB-factor sharpened map of human AP-3 in the Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: B-factor sharpened map of human AP-3 in the Apo state

Fileemd_45214_additional_4.map
AnnotationB-factor sharpened map of human AP-3 in the Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Filtered map of human AP-3 in the Apo state

Fileemd_45214_additional_5.map
AnnotationFiltered map of human AP-3 in the Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half map of human AP-3 in the Apo state

Fileemd_45214_half_map_1.map
AnnotationUnfiltered half map of human AP-3 in the Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half map of human AP-3 in the Apo state

Fileemd_45214_half_map_2.map
AnnotationUnfiltered half map of human AP-3 in the Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human Adaptor Protein Complex AP-3 in the Apo state

EntireName: Human Adaptor Protein Complex AP-3 in the Apo state
Components
  • Complex: Human Adaptor Protein Complex AP-3 in the Apo state
    • 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

-
Supramolecule #1: Human Adaptor Protein Complex AP-3 in the Apo state

SupramoleculeName: Human Adaptor Protein Complex AP-3 in the Apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 215 KDa

-
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: 66.164953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LQDLVRGIRN HKEDEAKYIS QCIDEIKQEL KQDNIAVKAN AVCKLTYLQM LGYDISWAAF NIIEVMSASK FTFKRIGYLA ASQSFHEGT DVIMLTTNQI RKDLSSPSQY DTGVALTGLS CFVTPDLARD LANDIMTLMS HTKPYIRKKA VLIMYKVFLK Y PESLRPAF ...String:
LQDLVRGIRN HKEDEAKYIS QCIDEIKQEL KQDNIAVKAN AVCKLTYLQM LGYDISWAAF NIIEVMSASK FTFKRIGYLA ASQSFHEGT DVIMLTTNQI 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 AGELN

UniProtKB: AP-3 complex subunit delta-1

-
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: 65.602797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DLKKNEDLKQ MLESNKDSAK LDAMKRIVGM IAKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPN QLIRASALRV LSSIRVPIIV PIMMLAIKEA SADLSPYVRK NAAHAIQKLY SLDPEQKEML IEVIEKLLKD K STLVAGSV ...String:
DLKKNEDLKQ MLESNKDSAK LDAMKRIVGM IAKGKNASEL FPAVVKNVAS KNIEIKKLVY VYLVRYAEEQ QDLALLSIST FQRALKDPN QLIRASALRV LSSIRVPIIV PIMMLAIKEA SADLSPYVRK NAAHAIQKLY SLDPEQKEML IEVIEKLLKD K STLVAGSV VMAFEEVCPD RIDLIHKNYR KLCNLLVDVE EWGQVVIIHM LTRYARTQFV SPWDPDHRLL IRNTKPLLQS RN AAVVMAV AQLYWHISPK SEAGIISKSL VRLLRSNREV QYIVLQNIAT MSIQRKGMFE PYLKSFYVRS TDPTMIKTLK LEI LTNLAN EANISTLLRE FQTYVKSQDK QFAAATIQTI GRCATNILEV TDTCLNGLVC LLSNRDEIVV AESVVVIKKL LQMQ PAQHG EIIKHMAKLL DSITVPVARA SILWLIGENC ERVPKIAPDV LRKMAKSFTS EDDLVKLQIL NLGAKLYLTN SKQTK LLTQ YILNLGKYDQ NYDIRDRTRF IRQLIVPNVK SGALSKYAKK IFLAQKPAPL LESPFKDRDH FQLGTLSHTL NIKATG YLE LSNWPEVAPD PSVRN

UniProtKB: AP-3 complex subunit beta-1

-
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: 14.274275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIHSLFLINC SGDIFLEKHW KSVVSQSVCD YFFEAQEKAA DVENVPPVIS TPHHYLISIY RDKLFFVSVI QTEVPPLFVI EFLHRVADT FQDYFGECSE AAIKDNVVIV YELLEEMLDN GFPLA

UniProtKB: AP-3 complex subunit mu-1

-
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: 17.412949 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIKAILIFNN HGKPRLSKFY QPYSEDTQQQ IIRETFHLVS KRDENVCNFL EGGLLIGGSD NKLIYRHYAT LYFVFCVDSS ESELGILDL IQVFVETLDK CFENVCELDL IFHVDKVHNI LAEMVMGGMV LETNMNEIVT QIDAQNKLEK SE

UniProtKB: AP-3 complex subunit sigma-1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 cleaned. 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)

-
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: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 1205158
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)

-
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-9c5c:
Structure of Human Adaptor Protein Complex AP-3 in the Apo State

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more