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- EMDB-71913: Structure of AP-2 bound to the dileucine motif and WxxPhi motif o... -

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Entry
Database: EMDB / ID: EMD-71913
TitleStructure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32; focused refinement 3
Map dataB-factor sharpened map
Sample
  • Complex: Structure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32
    • Protein or peptide: AP-2 complex subunit alpha-2
    • Protein or peptide: AP-2 complex subunit beta
    • Protein or peptide: AP-2 complex subunit mu
    • Protein or peptide: AP-2 complex subunit sigma
    • Protein or peptide: Coiled-coil domain-containing protein 32
KeywordsClathin / AP-2 adaptor complex / CCDC32 / assembly chaperone / ENDOCYTOSIS
Function / homology
Function and homology information


Formation of annular gap junctions / Gap junction degradation / regulation of clathrin-dependent endocytosis / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation ...Formation of annular gap junctions / Gap junction degradation / regulation of clathrin-dependent endocytosis / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD4 / head development / Trafficking of GluR2-containing AMPA receptors / clathrin coat / VLDLR internalisation and degradation / cardiac septum development / clathrin adaptor complex / MHC class II antigen presentation / extrinsic component of presynaptic endocytic zone membrane / Recycling pathway of L1 / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / cilium organization / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / membrane coat / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin coat assembly / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / clathrin-cargo adaptor activity / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / coronary vasculature development / positive regulation of protein localization to membrane / neurotransmitter secretion / regulation of hematopoietic stem cell differentiation / ventricular septum development / aorta development / low-density lipoprotein particle receptor binding / clathrin binding / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / positive regulation of endocytosis / negative regulation of protein localization to plasma membrane / synaptic vesicle endocytosis / vesicle-mediated transport / Neutrophil degranulation / clathrin-coated pit / phosphatidylinositol binding / secretory granule / protein serine/threonine kinase binding / kidney development / intracellular protein transport / receptor internalization / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / synaptic vesicle / heart development / protein-containing complex assembly / cytoplasmic vesicle / transmembrane transporter binding / postsynapse / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / mitochondrion / plasma membrane
Similarity search - Function
Coiled-coil domain containing protein 32 / Coiled-coil domain containing 32 / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain ...Coiled-coil domain containing protein 32 / Coiled-coil domain containing 32 / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / 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 / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / AP complex subunit beta / Clathrin adaptor complexes medium chain signature 1. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / AP-2 complex subunit mu, C-terminal superfamily / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit mu / Coiled-coil domain-containing protein 32 / AP-2 complex subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBaker RW / Kikkawa M / Sloan DE / Yanagisawa H
Funding support United States, Japan, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150960 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)F31DE034311 United States
Japan Society for the Promotion of Science (JSPS)SP24007 Japan
Japan Society for the Promotion of Science (JSPS)21H04762 Japan
Japan Society for the Promotion of Science (JSPS)21H05248 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA016086 United States
CitationJournal: To Be Published
Title: Structure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32; focused refinement 3
Authors: Baker RW / Kikkawa M / Sloan DE / Yanagisawa H
History
DepositionAug 4, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71913.png

Downloads & links

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Map

FileDownload / File: emd_71913.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å		0.88 Å/pix.
x 300 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.6023089 - 2.8577223
Average (Standard dev.)0.00068675575 (±0.025600327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 262.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71913_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Mask #2

Fileemd_71913_msk_2.map
Projections & Slices
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Additional map: Map filtered by local resolution

Fileemd_71913_additional_1.map
AnnotationMap filtered by local resolution
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_71913_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locres file for coloring by local resolution

Fileemd_71913_additional_3.map
AnnotationLocres file for coloring by local resolution
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Half map: Half map 2

Fileemd_71913_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_71913_half_map_2.map
AnnotationHalf map 1
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Sample components

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Entire : Structure of AP-2 bound to the dileucine motif and WxxPhi motif o...

EntireName: Structure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32
Components
  • Complex: Structure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32
    • Protein or peptide: AP-2 complex subunit alpha-2
    • Protein or peptide: AP-2 complex subunit beta
    • Protein or peptide: AP-2 complex subunit mu
    • Protein or peptide: AP-2 complex subunit sigma
    • Protein or peptide: Coiled-coil domain-containing protein 32

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Supramolecule #1: Structure of AP-2 bound to the dileucine motif and WxxPhi motif o...

SupramoleculeName: Structure of AP-2 bound to the dileucine motif and WxxPhi motif of CCDC32
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: AP-2 complex subunit alpha-2

MacromoleculeName: AP-2 complex subunit alpha-2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPAVSKGDGM RGLAVFISDI RNCKSKEAEI KRINKELANI RSKFKGDKAL DGYSKKKYVC KLLFIFLLGH DIDFGHMEAV NLLSSNRYTE KQIGYLFISV LVNSNSELIR LINNAIKNDL ASRNPTFMGL ALHCIANVGS REMAEAFAGE IPKILVAGDT MDSVKQSAAL ...String:
MPAVSKGDGM RGLAVFISDI RNCKSKEAEI KRINKELANI RSKFKGDKAL DGYSKKKYVC KLLFIFLLGH DIDFGHMEAV NLLSSNRYTE KQIGYLFISV LVNSNSELIR LINNAIKNDL ASRNPTFMGL ALHCIANVGS REMAEAFAGE IPKILVAGDT MDSVKQSAAL CLLRLYRTSP DLVPMGDWTS RVVHLLNDQH LGVVTAATSL ITTLAQKNPE EFKTSVSLAV SRLSRIVTSA STDLQDYTYY FVPAPWLSVK LLRLLQCYPP PEDPAVRGRL TECLETILNK AQEPPKSKKV QHSNAKNAVL FEAISLIIHH DSEPNLLVRA CNQLGQFLQH RETNLRYLAL ESMCTLASSE FSHEAVKTHI ETVINALKTE RDVSVRQRAV DLLYAMCDRS NAQQIVAEML SYLETADYSI REEIVLKVAI LAEKYAVDYT WYVDTILNLI RIAGDYVSEE VWYRVIQIVI NRDDVQGYAA KTVFEALQAP ACHENLVKVG GYILGEFGNL IAGDPRSSPL IQFNLLHSKF HLCSVPTRAL LLSTYIKFVN LFPEVKATIQ DVLRSDSQLK NADVELQQRA VEYLRLSTVA STDILATVLE EMPPFPERES SILAKLKKKK GGSGLEVLFQ

UniProtKB: AP-2 complex subunit alpha-2

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Macromolecule #2: AP-2 complex subunit beta

MacromoleculeName: AP-2 complex subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDSKYFTTN KKGEIFELKA ELNNEKKEKR KEAVKKVIAA MTVGKDVSSL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVNS FVKDCEDPNP LIRALAVRTM GCIRVDKITE YLCEPLRKCL KDEDPYVRKT AAVCVAKLHD INAQMVEDQG FLDSLRDLIA ...String:
MTDSKYFTTN KKGEIFELKA ELNNEKKEKR KEAVKKVIAA MTVGKDVSSL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVNS FVKDCEDPNP LIRALAVRTM GCIRVDKITE YLCEPLRKCL KDEDPYVRKT AAVCVAKLHD INAQMVEDQG FLDSLRDLIA DSNPMVVANA VAALSEISES HPNSNLLDLN PQNINKLLTA LNECTEWGQI FILDCLSNYN PKDDREAQSI CERVTPRLSH ANSAVVLSAV KVLMKFLELL PKDSDYYNML LKKLAPPLVT LLSGEPEVQY VALRNINLIV QKRPEILKQE IKVFFVKYND PIYVKLEKLD IMIRLASQAN IAQVLAELKE YATEVDVDFV RKAVRAIGRC AIKVEQSAER CVSTLLDLIQ TKVNYVVQEA IVVIRDIFRK YPNKYESIIA TLCENLDSLD EPDARAAMIW IVGEYAERID NADELLESFL EGFHDESTQV QLTLLTAIVK LFLKKPSETQ ELVQQVLSLA TQDSDNPDLR DRGYIYWRLL STDPVTAKEV VLSEKPLISE ETDLIEPTLL DELICHIGSL ASVYHKPPNA FVEGSHGIHR K

UniProtKB: AP-2 complex subunit beta

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Macromolecule #3: AP-2 complex subunit mu

MacromoleculeName: AP-2 complex subunit mu / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIGGLFIYNH KGEVLISRVY RDDIGRNAVD AFRVNVIHAR QQVRSPVTNI ARTSFFHVKR SNIWLAAVTK QNVNAAMVFE FLYKMCDVMA AYFGKISEEN IKNNFVLIYE LLDEILDFGY PQNSETGALK TFITQQGIKS QHQTKEEQSQ ITSQVTGQIG WRREGIKYRR ...String:
MIGGLFIYNH KGEVLISRVY RDDIGRNAVD AFRVNVIHAR QQVRSPVTNI ARTSFFHVKR SNIWLAAVTK QNVNAAMVFE FLYKMCDVMA AYFGKISEEN IKNNFVLIYE LLDEILDFGY PQNSETGALK TFITQQGIKS QHQTKEEQSQ ITSQVTGQIG WRREGIKYRR NELFLDVLES VNLLMSPQGQ VLSAHVSGRV VMKSYLSGMP ECKFGMNDKI VIEKQGKGTA DETSKSGKQS IAIDDCTFHQ CVRLSKFDSE RSISFIPPDG EFELMRYRTT KDIILPFRVI PLVREVGRTK LEVKVVIKSN FKPSLLAQKI EVRIPTPLNT SGVQVICMKG KAKYKASENA IVWKIKRMAG MKESQISAEI ELLPTNDKKK WARPPISMNF EVPFAPSGLK VRYLKVFEPK LNYSDHDVIK WVRYIGRSGI YETRC

UniProtKB: AP-2 complex subunit mu

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Macromolecule #4: AP-2 complex subunit sigma

MacromoleculeName: AP-2 complex subunit sigma / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIRFILIQNR AGKTRLAKWY MQFDDDEKQK LIEEVHAVVT VRDAKHTNFV EFRNFKIIYR RYAGLYFCIC VDVNDNNLAY LEAIHNFVEV LNEYFHNVCE LDLVFNFYKV YTVVDEMFLA GEIRETSQTK VLKQLLMLQS LE

UniProtKB: AP-2 complex subunit sigma

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Macromolecule #5: Coiled-coil domain-containing protein 32

MacromoleculeName: Coiled-coil domain-containing protein 32 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKMFESLDSS ATKSGRDLWA EICSCLPSPA QEDVSDNAFS DSFMDSHPAG ESHTAAADSA VQPAGKPWAP LHDSEVYLAS LEKKLRRIKG LNEEVTSKDM LRTLAQAKKE CWDRFLQEKL ASEFFVDGLD SDERTLEHFK RWLQPDKVAI STEEVQFLIP PESQAEKPEA GDKPAAAEQ

UniProtKB: Coiled-coil domain-containing protein 32

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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

Concentration0.4 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 65489 / Average exposure time: 2.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 80000

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio model generation in cryosparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Details: Non-uniform refinement; local refinement / Number images used: 97343
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model

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