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- PDB-9qpq: The structure of the COPI leaf bound to GOLPH3 -

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Basic information

Entry
Database: PDB / ID: 9qpq
TitleThe structure of the COPI leaf bound to GOLPH3
Components
  • (Coatomer subunit ...) x 6
  • ADP-ribosylation factor 1
  • Golgi phosphoprotein 3
KeywordsSTRUCTURAL PROTEIN / COPI coated vesicles / GOLPH3 / Golgi transport / vesicular transport
Function / homology
Function and homology information


asymmetric Golgi ribbon formation / protein targeting to Golgi apparatus / cargo adaptor activity / cerebellar Purkinje cell layer maturation / protein localization to axon / protein localization to cell leading edge / Golgi vesicle budding / COPI-coated vesicle / pancreatic juice secretion / Golgi cisterna ...asymmetric Golgi ribbon formation / protein targeting to Golgi apparatus / cargo adaptor activity / cerebellar Purkinje cell layer maturation / protein localization to axon / protein localization to cell leading edge / Golgi vesicle budding / COPI-coated vesicle / pancreatic juice secretion / Golgi cisterna / cellular response to rapamycin / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / COPI-mediated anterograde transport / COPI vesicle coat / glycoprotein biosynthetic process / protein retention in Golgi apparatus / Glycosphingolipid transport / Golgi vesicle transport / regulation of receptor internalization / Intra-Golgi traffic / COPI-dependent Golgi-to-ER retrograde traffic / regulation of Arp2/3 complex-mediated actin nucleation / Golgi ribbon formation / organelle transport along microtubule / Synthesis of PIPs at the Golgi membrane / establishment of Golgi localization / cell adhesion molecule production / leukocyte tethering or rolling / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Nef Mediated CD4 Down-regulation / Golgi to plasma membrane protein transport / dendritic spine organization / phosphatidylinositol-4-phosphate binding / regulation of mitochondrion organization / long-term synaptic depression / lamellipodium assembly / COPI-dependent Golgi-to-ER retrograde traffic / Golgi cisterna membrane / Lysosome Vesicle Biogenesis / pigmentation / Golgi Associated Vesicle Biogenesis / endoplasmic reticulum-Golgi intermediate compartment / Golgi organization / Synthesis of PIPs at the plasma membrane / cell leading edge / protein secretion / intracellular copper ion homeostasis / positive regulation of TOR signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / Neutrophil degranulation / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / adult locomotory behavior / small monomeric GTPase / positive regulation of protein secretion / intracellular protein transport / trans-Golgi network / establishment of localization in cell / hormone activity / cellular response to virus / mitochondrial intermembrane space / cell migration / protein transport / growth cone / gene expression / neuron projection / endosome / postsynaptic density / Golgi membrane / protein domain specific binding / axon / focal adhesion / neuronal cell body / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / negative regulation of apoptotic process / GTP binding / structural molecule activity / enzyme binding / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Golgi phosphoprotein 3-like / Golgi phosphoprotein 3-like domain superfamily / Golgi phosphoprotein 3 (GPP34) / Coatomer beta subunit, C-terminal / Coatomer beta subunit (COPB1) / Coatomer beta subunit, appendage platform domain / Coatomer beta C-terminal region / Coatomer beta subunit appendage platform / Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit ...Golgi phosphoprotein 3-like / Golgi phosphoprotein 3-like domain superfamily / Golgi phosphoprotein 3 (GPP34) / Coatomer beta subunit, C-terminal / Coatomer beta subunit (COPB1) / Coatomer beta subunit, appendage platform domain / Coatomer beta C-terminal region / Coatomer beta subunit appendage platform / Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit / Coatomer subunit gamma, C-terminal / Coatomer, gamma subunit, appendage domain superfamily / Coatomer subunit zeta / Coatomer gamma subunit appendage platform subdomain / Coatomer subunit gamma-1 C-terminal appendage platform / Coatomer delta subunit / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / ADP-ribosylation factor 1-5 / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / 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. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / TBP domain superfamily / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / WD domain, G-beta repeat / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Coatomer subunit beta' / Coatomer subunit zeta-1 / ADP-ribosylation factor 1 / Coatomer subunit delta / Coatomer subunit alpha / Golgi phosphoprotein 3 / Coatomer subunit beta / Coatomer subunit gamma-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.5 Å
AuthorsTaylor, R.J. / Tagiltsev, G. / Ciazynska, K.A. / Briggs, J.A.G.
Funding support Germany, United Kingdom, European Union, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
Medical Research Council (MRC, United Kingdom)MC_U105178783 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
Wellcome Trust227915/Z/23/Z United Kingdom
European Molecular Biology Organization (EMBO)ALTF-383-2022European Union
CitationJournal: Sci Adv / Year: 2025
Title: The mechanistic basis of cargo selection during Golgi maturation.
Authors: Rebecca J Taylor / Nikita Zubkov / Katarzyna A Ciazynska / Jonathan G G Kaufman / Grigory Tagiltsev / David J Owen / John A G Briggs / Sean Munro /
Abstract: The multiple cisternae of the Golgi apparatus contain resident membrane proteins crucial for lipid and protein glycosylation. How Golgi residents remain in their designated compartments despite a ...The multiple cisternae of the Golgi apparatus contain resident membrane proteins crucial for lipid and protein glycosylation. How Golgi residents remain in their designated compartments despite a constant flow of secretory cargo is incompletely understood. Here, we determine the structure of the COPI vesicle coat containing GOLPH3, an adaptor protein that binds the cytosolic tails of many Golgi residents. Analysis of this structure, together with structure-guided mutagenesis and functional assays, reveals how GOLPH3 uses coincidence detection of COPI and lipids to engage Golgi residents preferentially at late cisternae. Our findings rationalize the logic of cisternal maturation and explain how COPI can engage different types of substrates in different Golgi cisternae to retrieve some proteins back to the ER while retaining others within the Golgi apparatus.
History
DepositionMar 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Golgi phosphoprotein 3
B: Golgi phosphoprotein 3
D: Coatomer subunit alpha
E: Coatomer subunit alpha
F: Coatomer subunit beta'
G: Coatomer subunit beta'
H: Coatomer subunit beta
I: Coatomer subunit beta
J: Coatomer subunit beta
K: Coatomer subunit beta
L: Coatomer subunit delta
M: Coatomer subunit gamma-1
N: Coatomer subunit gamma-1
O: Coatomer subunit gamma-1
P: Coatomer subunit zeta-1
R: ADP-ribosylation factor 1
S: ADP-ribosylation factor 1
T: ADP-ribosylation factor 1


Theoretical massNumber of molelcules
Total (without water)1,411,43418
Polymers1,411,43418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 5 molecules ABRST

#1: Protein Golgi phosphoprotein 3 / Coat protein GPP34 / Mitochondrial DNA absence factor / MIDAS


Mass: 33859.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOLPH3, GPP34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4A6
#8: Protein ADP-ribosylation factor 1


Mass: 20721.742 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84077, small monomeric GTPase

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Coatomer subunit ... , 6 types, 13 molecules DEFGHIJKLMNOP

#2: Protein Coatomer subunit alpha / Alpha-coat protein / Alpha-COP


Mass: 138617.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Copa / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q8CIE6
#3: Protein Coatomer subunit beta' / Beta'-coat protein / Beta'-COP / p102


Mass: 102566.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Copb2 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O55029
#4: Protein
Coatomer subunit beta / Beta-coat protein / Beta-COP


Mass: 107197.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Copb1, Copb / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9JIF7
#5: Protein Coatomer subunit delta / Archain / Delta-coat protein / Delta-COP


Mass: 57304.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arcn1, Copd / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5XJY5
#6: Protein Coatomer subunit gamma-1 / Gamma-1-coat protein / Gamma-1-COP


Mass: 97622.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Copg1, Copg / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9QZE5
#7: Protein Coatomer subunit zeta-1 / Zeta-1-coat protein / Zeta-1 COP


Mass: 20218.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Copz1, Copz / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61924

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Reconstitution of COPI-coated vesicles containing the cargo adaptor protein GOLPH3COMPLEXall0RECOMBINANT
2Mus musculus COPI coatomer complex, recombinantly expressed in insect cells and purifiedCOMPLEX#2-#71RECOMBINANT
3Homo sapiens GOLPH3, recombinantly expressed in E. coli and purifiedCOMPLEX#11RECOMBINANT
4Homo sapiens Arf1, recombinantly expressed in E. coli and purifiedCOMPLEX#81RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
33
44
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Mus musculus (house mouse)10090
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Trichoplusia ni (cabbage looper)7111
32Trichoplusia ni (cabbage looper)7111
43Escherichia coli (E. coli)562
54Escherichia coli (E. coli)562
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESHEPES1
2125 mMPotassium acetateKAc1
32.5 mMMagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Budded and budding COPI vesicles were reconstituted by mixing liposomes with purified COPI coat protein, Arf1, GTPgammaS, and GOLPH3.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 53000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.114 e/Å2 / Avg electron dose per subtomogram: 125 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 1

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Processing

EM software
IDNameVersionCategoryDetails
1subTOMv1.1.5volume selectionhttps://github.com/DustinMorado/subTOM
4NOVACTFCTF correction
7UCSF ChimeraX1.9model fitting
10RELIONv3.0final Euler assignment
12RELIONv3.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108432 / Symmetry type: POINT
EM volume selectionDetails: A total of 4866 COPI vesicles and buds were manually picked from 206 tomograms in UCSF Chimera. The center of each coated vesicle or bud was picked and radii were assigned using a custom- ...Details: A total of 4866 COPI vesicles and buds were manually picked from 206 tomograms in UCSF Chimera. The center of each coated vesicle or bud was picked and radii were assigned using a custom-written plugin (https://www.biochem.mpg.de/7940000/Pick-Particle). Initial coordinates for subsequent particle search were seeded with an even spacing of 10.9 nm (8 pixels in tomograms binned 8 times) perpendicular to the sphere surface, and with random in-plane rotation, yielding a total of 193104 particles (C3).
Num. of tomograms: 206 / Num. of volumes extracted: 193104 / Reference model: EMDB-2985
Atomic model buildingB value: 200 / Protocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Source name: AlphaFold / Type: in silico model

IDAccession codeChain residue rangeInitial refinement model-IDDetails
1Q8CIE61-8241
2O550291-8382
3Q9JIF71-71031-499; 536-710
4Q5XJ751-24741-177; 224-247
5Q9QZE51-5825
6P619246-1506
7P8407715-1817
8Q9H4A610-290810-25; 55-298

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