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- EMDB-16804: AP2 bound to MSP1E3D1 nanodisc with Tgn38 cargo peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-16804
TitleAP2 bound to MSP1E3D1 nanodisc with Tgn38 cargo peptide
Map datafull map
Sample
  • Complex: AP2 bound to MSP1E3D1 nanodisc and Tgn38 cargo peptide
    • Complex: AP-2 complex
      • 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
    • Complex: Tgn38 cargo peptide
      • Protein or peptide: Tgn38
KeywordsClathrin-mediated endocytosis / peripheral membrane protein / ENDOCYTOSIS
Function / homology
Function and homology information


postsynaptic Golgi apparatus / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Retrograde transport at the Trans-Golgi-Network / Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance ...postsynaptic Golgi apparatus / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Retrograde transport at the Trans-Golgi-Network / Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / WNT5A-dependent internalization of FZD4 / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / clathrin coat / extrinsic component of presynaptic endocytic zone membrane / VLDLR internalisation and degradation / Golgi to endosome transport / Golgi Associated Vesicle Biogenesis / cardiac septum development / MHC class II antigen presentation / Recycling pathway of L1 / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / membrane coat / vesicle budding from membrane / clathrin-dependent endocytosis / trans-Golgi network transport vesicle / coronary vasculature development / MHC class II antigen presentation / positive regulation of protein localization to membrane / neurotransmitter receptor internalization / signal sequence binding / regulation of hematopoietic stem cell differentiation / aorta development / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / positive regulation of receptor internalization / Trafficking of GluR2-containing AMPA receptors / positive regulation of endocytosis / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / protein serine/threonine kinase binding / vesicle-mediated transport / Neutrophil degranulation / phosphatidylinositol binding / kidney development / secretory granule / intracellular protein transport / trans-Golgi network / kinase binding / cytoplasmic side of plasma membrane / disordered domain specific binding / synaptic vesicle / heart development / cytoplasmic vesicle / protein-containing complex assembly / transmembrane transporter binding / postsynapse / endosome / protein domain specific binding / intracellular membrane-bounded organelle / lipid binding / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / Golgi apparatus / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Keratinocyte-associated gene product / 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 / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain ...Keratinocyte-associated gene product / 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 / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / 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. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Mu homology domain / Adaptin C-terminal domain / Mu homology domain (MHD) profile. / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / 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 / Trans-Golgi network integral membrane protein TGN38 / AP-2 complex subunit sigma / AP-2 complex subunit mu / AP-2 complex subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsBaker RW / Sarsam R / Cannon KS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Struct Biol / Year: 2023
Title: Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins.
Authors: Kevin S Cannon / Reta D Sarsam / Tanita Tedamrongwanish / Kevin Zhang / Richard W Baker /
Abstract: Peripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as signal transduction, membrane trafficking, and autophagy. Transient ...Peripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as signal transduction, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported high-resolution structures of peripheral membrane proteins bound to the membrane. We analyzed the utility of lipid nanodiscs to serve as a template for cryo-EM analysis of peripheral membrane proteins. We tested a variety of nanodiscs and we report a 3.3 Å structure of the AP2 clathrin adaptor complex bound to a 17-nm nanodisc, with sufficient resolution to visualize a bound lipid head group. Our data demonstrate that lipid nanodiscs are amenable to high-resolution structure determination of peripheral membrane proteins and provide a framework for extending this analysis to other systems.
History
DepositionMar 7, 2023-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16804.png

Downloads & links

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Map

FileDownload / File: emd_16804.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 192 pix.
= 337.92 Å		1.76 Å/pix.
x 192 pix.
= 337.92 Å		1.76 Å/pix.
x 192 pix.
= 337.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6114211 - 1.5467027
Average (Standard dev.)0.000641149 (±0.03712365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16804_msk_1.map
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Additional map: cryoSPARC sharpened map

Fileemd_16804_additional_1.map
AnnotationcryoSPARC sharpened map
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Additional map: map for coloring my local resolution

Fileemd_16804_additional_2.map
Annotationmap for coloring my local resolution
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Additional map: locally filtered map

Fileemd_16804_additional_3.map
Annotationlocally filtered map
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Additional map: deepEMhancer sharpened map

Fileemd_16804_additional_4.map
AnnotationdeepEMhancer sharpened map
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Half map: half map 2

Fileemd_16804_half_map_1.map
Annotationhalf map 2
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Half map: half map 2

Fileemd_16804_half_map_2.map
Annotationhalf map 2
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Sample components

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Entire : AP2 bound to MSP1E3D1 nanodisc and Tgn38 cargo peptide

EntireName: AP2 bound to MSP1E3D1 nanodisc and Tgn38 cargo peptide
Components
  • Complex: AP2 bound to MSP1E3D1 nanodisc and Tgn38 cargo peptide
    • Complex: AP-2 complex
      • 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
    • Complex: Tgn38 cargo peptide
      • Protein or peptide: Tgn38

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Supramolecule #1: AP2 bound to MSP1E3D1 nanodisc and Tgn38 cargo peptide

SupramoleculeName: AP2 bound to MSP1E3D1 nanodisc and Tgn38 cargo peptide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Nanodiscs were assembled with a lipid mixture containing 73 mol% DOPC, 15 mol% DOPS, 10 mol% PIP2, 2 mol% Tgn38 cargo peptide. Complex was formed by co-elution via gel filtration chromatography.
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: AP-2 complex

SupramoleculeName: AP-2 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / Details: AP-2 complex
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Tgn38 cargo peptide

SupramoleculeName: Tgn38 cargo peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5 / Details: Tgn38 cargo peptide

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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 DETSKS GKQ SIAIDDCTFH QCVRLSKFDS ERSISFIPPD GEFELMRYRT TKDIILPFRV IPLVREVGRT KLEVKVVIKS NFKPSLL AQ KIEVRIPTPL NTSGVQVICM KGKAKYKASE NAIVWKIKRM AGMKESQISA EIELLPTNDK KKWARPPISM NFEVPFAP S GLKVRYLKVF EPKLNYSDHD VIKWVRYIGR SGIYETRC

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 LEAIHNFVE VLNEYFHNVC ELDLVFNFYK VYTVVDEMFL AGEIRETSQT KVLKQLLMLQ SLE

UniProtKB: AP-2 complex subunit sigma

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Macromolecule #5: Tgn38

MacromoleculeName: Tgn38 / type: protein_or_peptide / ID: 5 / Details: N-terminal oleic acid and FITC moieties / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString:
KVTRRPKASD YQRL

UniProtKB: Trans-Golgi network integral membrane protein TGN38

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES pH 7.4, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Details: Tergeo EM plasma cleaner
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Two sample applications..
DetailsNanodiscs were assembled with a lipid mixture containing 73 mol% DOPC, 15 mol% DOPS, 10 mol% PIP2, 2 mol% Tgn38 cargo peptide. Complex was formed by co-elution via gel filtration chromatography.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 45000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsData collected in counting mode.
Particle selectionNumber selected: 2800000
Details: General model gmodel_phosnet_202005_N63_c17.h5 used for crYOLO picking.
Startup modelType of model: OTHER / Details: Ab inition model generation in cryoSPARC v3.2.
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 62324
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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