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- EMDB-63969: ARF1(Q71L) bound M4-CTD-docked AP-4 core -

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Basic information

Entry
Database: EMDB / ID: EMD-63969
TitleARF1(Q71L) bound M4-CTD-docked AP-4 core
Map data
Sample
  • Complex: ARF1 bound M4-CTD-docked AP-4 core
    • Protein or peptide: AP-4 complex subunit beta-1
    • Protein or peptide: AP-4 complex subunit epsilon-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-4 complex subunit mu-1
    • Protein or peptide: AP-4 complex subunit sigma-1
KeywordsAdaptor protein complex / TRANSPORT PROTEIN
Function / homology
Function and homology information


protein localization to somatodendritic compartment / cytoplasmic side of trans-Golgi network transport vesicle membrane / AP-4 adaptor complex / protein localization to basolateral plasma membrane / cargo adaptor activity / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Glycosphingolipid transport ...protein localization to somatodendritic compartment / cytoplasmic side of trans-Golgi network transport vesicle membrane / AP-4 adaptor complex / protein localization to basolateral plasma membrane / cargo adaptor activity / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Glycosphingolipid transport / regulation of receptor internalization / Golgi to lysosome transport / Intra-Golgi traffic / Golgi to endosome transport / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / protein targeting to lysosome / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / clathrin binding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Synthesis of PIPs at the plasma membrane / cell leading edge / transmembrane protein transporter activity / intracellular copper ion homeostasis / autophagosome assembly / protein targeting / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / endosome lumen / sarcomere / trans-Golgi network membrane / small monomeric GTPase / trans-Golgi network / intracellular protein transport / cellular response to virus / intracellular protein localization / protein transport / G protein activity / cytoplasmic vesicle / early endosome / neuron projection / postsynaptic density / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Adaptor protein complex AP-4, epsilon subunit / AP-4 complex subunit epsilon-1, C-terminal / Adaptin AP4 complex epsilon appendage platform / Adaptin AP4 complex epsilon appendage platform / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain ...Adaptor protein complex AP-4, epsilon subunit / AP-4 complex subunit epsilon-1, C-terminal / Adaptin AP4 complex epsilon appendage platform / Adaptin AP4 complex epsilon appendage platform / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / ADP-ribosylation factor 1-5 / AP complex subunit beta / 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 / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Longin-like domain superfamily / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / TBP domain superfamily / 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-4 complex subunit mu-1 / ADP-ribosylation factor 1 / AP-4 complex subunit epsilon-1 / AP-4 complex subunit sigma-1 / AP-4 complex subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / Resolution: 6.8 Å
AuthorsWang YH / Li W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for the dynamic conformations of AP-4 and its association with ARF1.
Authors: Yanghui Wang / Wei Li / Yunlong Qiu / Si Wu / Liu Hong / Yan Zhao / Wei Feng /
Abstract: Among the distinct adaptor protein (AP) complexes, AP-4 primarily functions as a non-clathrin-coated vesicle machinery essential for intracellular membrane trafficking. ARF1 is a master regulator of ...Among the distinct adaptor protein (AP) complexes, AP-4 primarily functions as a non-clathrin-coated vesicle machinery essential for intracellular membrane trafficking. ARF1 is a master regulator of AP-4 membrane recruitment, but the underlying mechanism remains elusive. Here, we present the cryo-EM structures of soluble AP-4 and the AP-4/ARF1 complex. Unexpectedly, AP-4 adopts a dynamic equilibrium between closed and open conformations, caused by loose contacts between its medium subunit and central core. ARF1 binding induces only subtle changes in AP-4, which retains its conformational equilibrium. Mutations at the AP-4/ARF1 interface disrupt complex formation and impair ARF1-dependent membrane recruitment. Efficient membrane recruitment of AP-4 likely requires the synergistic engagement of ARF1 and cargoes. Disrupting the conformational flexibility of AP-4 interferes with this synergistic effect and compromises AP-4-mediated membrane trafficking. Our findings may redefine AP-4 as a conformationally dynamic complex modulated by cooperative interactions, providing insights into neurodevelopmental disorders associated with AP-4 dysfunction.
History
DepositionMar 29, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63969.png

Downloads & links

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Map

FileDownload / File: emd_63969.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.629
Minimum - Maximum-2.0489786 - 3.336275
Average (Standard dev.)0.0011033064 (±0.09067981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63969_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Half map: #1

Fileemd_63969_half_map_2.map
Projections & Slices
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Sample components

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Entire : ARF1 bound M4-CTD-docked AP-4 core

EntireName: ARF1 bound M4-CTD-docked AP-4 core
Components
  • Complex: ARF1 bound M4-CTD-docked AP-4 core
    • Protein or peptide: AP-4 complex subunit beta-1
    • Protein or peptide: AP-4 complex subunit epsilon-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-4 complex subunit mu-1
    • Protein or peptide: AP-4 complex subunit sigma-1

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Supramolecule #1: ARF1 bound M4-CTD-docked AP-4 core

SupramoleculeName: ARF1 bound M4-CTD-docked AP-4 core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: AP-4 complex subunit beta-1

MacromoleculeName: AP-4 complex subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.162699 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPYLGSEDVV KELKKALCNP HIQADRLRYR NVIQRVIRYM TQGLDMSGVF MEMVKASATV DIVQKKLVYL YMCTYAPLKP DLALLAINT LCKDCSDPNP MVRGLALRSM CSLRMPGVQE YIQQPILNGL RDKASYVRRV AVLGCAKMHN LHGDSEVDGA L VNELYSLL ...String:
MPYLGSEDVV KELKKALCNP HIQADRLRYR NVIQRVIRYM TQGLDMSGVF MEMVKASATV DIVQKKLVYL YMCTYAPLKP DLALLAINT LCKDCSDPNP MVRGLALRSM CSLRMPGVQE YIQQPILNGL RDKASYVRRV AVLGCAKMHN LHGDSEVDGA L VNELYSLL RDQDPIVVVN CLRSLEEILK QEGGVVINKP IAHHLLNRMS KLDQWGQAEV LNFLLRYQPR SEEELFDILN LL DSFLKSS SPGVVMGATK LFLILAKMFP HVQTDVLVRV KGPLLAACSS ESRELCFVAL CHVRQILHSL PGHFSSHYKK FFC SYSEPH YIKLQKVEVL CELVNDENVQ QVLEELRGYC TDVSADFAQA AIFAIGGIAR TYTDQCVQIL TELLGLRQEH ITTV VVQTF RDLVWLCPQC TEAVCQALPG CEENIQDSEG KQALIWLLGV HGERIPNAPY VLEDFVENVK SETFPAVKME LLTAL LRLF LSRPAECQDM LGRLLYYCIE EEKDMAVRDR GLFYYRLLLV GIDEVKRILC SPKSDPTLGL LEDPAERPVN SWASDF NTL VPVYGKAHWA TIS

UniProtKB: AP-4 complex subunit beta-1

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Macromolecule #2: AP-4 complex subunit epsilon-1

MacromoleculeName: AP-4 complex subunit epsilon-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.470781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDIVEKTLT ALPGLFLQNQ PGGGPAAAKA SFSSRLGSLV RGITALTSKH EEEKLIQQEL SSLKATVSAP TTTLKMMKEC MVRLIYCEM LGYDASFGYI HAIKLAQQGN LLEKRVGYLA VSLFLHESHE LLLLLVNTVV KDLQSTNLVE VCMALTVVSQ I FPCEMIPA ...String:
MSDIVEKTLT ALPGLFLQNQ PGGGPAAAKA SFSSRLGSLV RGITALTSKH EEEKLIQQEL SSLKATVSAP TTTLKMMKEC MVRLIYCEM LGYDASFGYI HAIKLAQQGN LLEKRVGYLA VSLFLHESHE LLLLLVNTVV KDLQSTNLVE VCMALTVVSQ I FPCEMIPA VLPLIEDKLQ HSKEIVRRKA VLALYKFHLI APNQVQHIHI KFRKALCDRD VGVMAASLHI YLRMIKENSS GY KDLTGSF VTILKQVVGG KLPVEFNYHS VPAPWLQIQL LRILGLLGKD DQRTSELMYD VLDESLRRAE LNHNVTYAIL FEC VHTVYS IYPKSELLEK AAKCIGKFVL SPKINLKYLG LKALTYVIQQ DPTLALQHQM TIIECLDHPD PIIKRETLEL LYRI TNAQN ITVIVQKMLE YLHQSKEEYV IVNLVGKIAE LAEKYAPDNA WFIQTMNAVF SVGGDVMHPD IPNNFLRLLA EGFDD ETED QQLRLYAVQS YLTLLDMENV FYPQRFLQVM SWVLGEYSYL LDKETPEEVI AKLYKLLMND SVSSETKAWL IAAVTK LTS QAHSSNTVER LIHEFTISLD TCMRQHAFEL KHLHENVELM KSLLPVDRS

UniProtKB: AP-4 complex subunit epsilon-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: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.807482 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MRILMVGLDA AGKTTILYKL KLGEIVTTIP TIGFNVETVE YKNISFTVWD VGGLDKIRPL WRHYFQNTQG LIFVVDSNDR ERVNEAREE LMRMLAEDEL RDAVLLVFAN KQDLPNAMNA AEITDKLGLH SLRHRNWYIQ ATCATSGDGL YEGLDWLSNQ L RNQK

UniProtKB: ADP-ribosylation factor 1

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

MacromoleculeName: AP-4 complex subunit mu-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.035887 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MISQFFILSS KGDPLIYKDF RGDSGGRDVA ELFYRKLTGL PGDESPVVMH HHGRHFIHIR HSGLYLVVTT SENVSPFSLL ELLSRLATL LGDYCGSLGE GTISRNVALV YELLDEVLDY GYVQTTSTEM LRNFIQTEAV VSKPFSLFDL SSVGLFGAET Q QSKVAPSS ...String:
MISQFFILSS KGDPLIYKDF RGDSGGRDVA ELFYRKLTGL PGDESPVVMH HHGRHFIHIR HSGLYLVVTT SENVSPFSLL ELLSRLATL LGDYCGSLGE GTISRNVALV YELLDEVLDY GYVQTTSTEM LRNFIQTEAV VSKPFSLFDL SSVGLFGAET Q QSKVAPSS AASRPVLSSR SDQSQKNEVF LDVVERLSVL IASNGSLLKV DVQGEIRLKS FLPSGSEMRI GLTEEFCVGK SE LRGYGPG IRVDEVSFHS SVNLDEFESH RILRLQPPQG ELTVMRYQLS DDLPSPLPFR LFPSVQWDRG SGRLQVYLKL RCD LLSKSQ ALNVRLHLPL PRGVVSLSQE LSSPEQKAEL AEGALRWDLP RVQGGSQLSG LFQMDVPGPP GPPSHGLSTS ASPL GLGPA SLSFELPRHT CSGLQVRFLR LAFRPCGNAN PHKWVRHLSH SDAYVIRI

UniProtKB: AP-4 complex subunit mu-1

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Macromolecule #5: AP-4 complex subunit sigma-1

MacromoleculeName: AP-4 complex subunit sigma-1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.023742 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MIKFFLMVNK QGQTRLSKYY EHVDINKRTL LETEVIKSCL SRSNEQCSFI EYKDFKLIYR QYAALFIVVG VNDTENEMAI YEFIHNFVE VLDEYFSRVS ELDIMFNLDK VHIILDEMVL NGCIVETNRA RILAPLLILD KMSES

UniProtKB: AP-4 complex subunit sigma-1

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1w63

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13372
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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