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- EMDB-63965: M4-CTD-undocked AP-4 core in apo form -

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Basic information

Entry
Database: EMDB / ID: EMD-63965
TitleM4-CTD-undocked AP-4 core in apo form
Map dataundocked-AP4 core
Sample
  • Complex: Hetero-tetrameric complex of AP-4 core
    • Protein or peptide: AP-4 complex subunit beta-1
    • Protein or peptide: AP-4 complex subunit epsilon-1
    • Protein or peptide: AP-4 complex subunit sigma-1
    • Protein or peptide: AP-4 complex subunit mu-1
Keywordsadaptor protein complex / cargo transportation / PROTEIN TRANSPORT
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 / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to lysosome transport / Golgi to endosome transport / protein targeting to lysosome ...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 / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to lysosome transport / Golgi to endosome transport / protein targeting to lysosome / clathrin binding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / transmembrane protein transporter activity / autophagosome assembly / protein targeting / vesicle-mediated transport / endosome lumen / trans-Golgi network membrane / trans-Golgi network / intracellular protein transport / intracellular protein localization / protein transport / cytoplasmic vesicle / early endosome / protein domain specific binding / extracellular exosome / 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 / 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. / Longin-like domain superfamily / TBP domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
AP-4 complex subunit mu-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: 4.0 Å
AuthorsWang YH / Li W
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
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 28, 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_63965.png

Downloads & links

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Map

FileDownload / File: emd_63965.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationundocked-AP4 core
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.386
Minimum - Maximum-1.1798074 - 2.1849275
Average (Standard dev.)0.00020227772 (±0.053112682)
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: undocked-AP4 core

Fileemd_63965_half_map_1.map
Annotationundocked-AP4 core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: undocked-AP4core

Fileemd_63965_half_map_2.map
Annotationundocked-AP4core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hetero-tetrameric complex of AP-4 core

EntireName: Hetero-tetrameric complex of AP-4 core
Components
  • Complex: Hetero-tetrameric complex of AP-4 core
    • Protein or peptide: AP-4 complex subunit beta-1
    • Protein or peptide: AP-4 complex subunit epsilon-1
    • Protein or peptide: AP-4 complex subunit sigma-1
    • Protein or peptide: AP-4 complex subunit mu-1

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Supramolecule #1: Hetero-tetrameric complex of AP-4 core

SupramoleculeName: Hetero-tetrameric complex of AP-4 core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 208 KDa

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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: 64.265664 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 VPVYG

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: AP-4 complex subunit sigma-1

MacromoleculeName: AP-4 complex subunit sigma-1 / type: protein_or_peptide / ID: 3 / 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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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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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: 53.0 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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 275020
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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