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- PDB-9u9i: M4-CTD-undocked AP-4 core in apo form -

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Basic information

Entry
Database: PDB / ID: 9u9i
TitleM4-CTD-undocked AP-4 core in apo form
Components
  • AP-4 complex subunit beta-1
  • AP-4 complex subunit epsilon-1
  • AP-4 complex subunit mu-1
  • AP-4 complex subunit sigma-1
KeywordsPROTEIN TRANSPORT / adaptor protein complex / cargo transportation
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 4 Å
AuthorsWang, Y.H. / Li, W.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: AP-4 complex subunit beta-1
E: AP-4 complex subunit epsilon-1
S: AP-4 complex subunit sigma-1
M: AP-4 complex subunit mu-1


Theoretical massNumber of molelcules
Total (without water)200,7964
Polymers200,7964
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein AP-4 complex subunit beta-1 / AP-4 adaptor complex subunit beta / Adaptor-related protein complex 4 subunit beta-1 / Beta subunit ...AP-4 adaptor complex subunit beta / Adaptor-related protein complex 4 subunit beta-1 / Beta subunit of AP-4 / Beta4-adaptin


Mass: 64265.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP4B1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y6B7
#2: Protein AP-4 complex subunit epsilon-1 / AP-4 adaptor complex subunit epsilon / Adaptor-related protein complex 4 subunit epsilon-1 / ...AP-4 adaptor complex subunit epsilon / Adaptor-related protein complex 4 subunit epsilon-1 / Epsilon subunit of AP-4 / Epsilon-adaptin


Mass: 69470.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP4E1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UPM8
#3: Protein AP-4 complex subunit sigma-1 / AP-4 adaptor complex subunit sigma-1 / Adaptor-related protein complex 4 subunit sigma-1 / Sigma-1 ...AP-4 adaptor complex subunit sigma-1 / Adaptor-related protein complex 4 subunit sigma-1 / Sigma-1 subunit of AP-4 / Sigma-4-adaptin / Sigma4-adaptin


Mass: 17023.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP4S1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y587
#4: Protein AP-4 complex subunit mu-1 / AP-4 adaptor complex mu subunit / Adaptor-related protein complex 4 subunit mu-1 / Mu subunit of AP- ...AP-4 adaptor complex mu subunit / Adaptor-related protein complex 4 subunit mu-1 / Mu subunit of AP-4 / Mu-adaptin-related protein 2 / mu-ARP2 / Mu4-adaptin / mu4


Mass: 50035.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP4M1, MUARP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00189
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hetero-tetrameric complex of AP-4 core / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.208 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275020 / Symmetry type: POINT
RefinementHighest resolution: 4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311175
ELECTRON MICROSCOPYf_angle_d0.6615121
ELECTRON MICROSCOPYf_dihedral_angle_d5.0091483
ELECTRON MICROSCOPYf_chiral_restr0.0411769
ELECTRON MICROSCOPYf_plane_restr0.0041906

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