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- EMDB-53278: The structure of the COPI leaf bound to GOLPH3 -

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Basic information

Entry
Database: EMDB / ID: EMD-53278
TitleThe structure of the COPI leaf bound to GOLPH3
Map dataCOPI heptameric leaf bound to GOLPH3 on membranes
Sample
  • Complex: Reconstitution of COPI-coated vesicles containing the cargo adaptor protein GOLPH3
    • Complex: Mus musculus COPI coatomer complex, recombinantly expressed in insect cells and purified
      • Protein or peptide: Coatomer subunit alpha
      • Protein or peptide: Coatomer subunit beta'
      • Protein or peptide: Coatomer subunit beta
      • Protein or peptide: Coatomer subunit delta
      • Protein or peptide: Coatomer subunit gamma-1
      • Protein or peptide: Coatomer subunit zeta-1
    • Complex: Homo sapiens GOLPH3, recombinantly expressed in E. coli and purified
      • Protein or peptide: Golgi phosphoprotein 3
    • Complex: Homo sapiens Arf1, recombinantly expressed in E. coli and purified
      • Protein or peptide: ADP-ribosylation factor 1
KeywordsCOPI coated vesicles / GOLPH3 / Golgi transport / vesicular transport / STRUCTURAL PROTEIN
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 speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 7.5 Å
AuthorsTaylor RJ / Tagiltsev G / Ciazynska KA / Briggs JAG
Funding support Germany, United Kingdom, European Union, 5 items
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, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53278.png

Downloads & links

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Map

FileDownload / File: emd_53278.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOPI heptameric leaf bound to GOLPH3 on membranes
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 292 pix.
= 499.32 Å		1.71 Å/pix.
x 292 pix.
= 499.32 Å		1.71 Å/pix.
x 292 pix.
= 499.32 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0053
Minimum - Maximum-0.023333697 - 0.042098027
Average (Standard dev.)0.00029214047 (±0.0015516926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions292292292
Spacing292292292
CellA=B=C: 499.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: COPI heptameric leaf bound to GOLPH3 on membranes

Fileemd_53278_half_map_1.map
AnnotationCOPI heptameric leaf bound to GOLPH3 on membranes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: COPI heptameric leaf bound to GOLPH3 on membranes

Fileemd_53278_half_map_2.map
AnnotationCOPI heptameric leaf bound to GOLPH3 on membranes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Reconstitution of COPI-coated vesicles containing the cargo adapt...

EntireName: Reconstitution of COPI-coated vesicles containing the cargo adaptor protein GOLPH3
Components
  • Complex: Reconstitution of COPI-coated vesicles containing the cargo adaptor protein GOLPH3
    • Complex: Mus musculus COPI coatomer complex, recombinantly expressed in insect cells and purified
      • Protein or peptide: Coatomer subunit alpha
      • Protein or peptide: Coatomer subunit beta'
      • Protein or peptide: Coatomer subunit beta
      • Protein or peptide: Coatomer subunit delta
      • Protein or peptide: Coatomer subunit gamma-1
      • Protein or peptide: Coatomer subunit zeta-1
    • Complex: Homo sapiens GOLPH3, recombinantly expressed in E. coli and purified
      • Protein or peptide: Golgi phosphoprotein 3
    • Complex: Homo sapiens Arf1, recombinantly expressed in E. coli and purified
      • Protein or peptide: ADP-ribosylation factor 1

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Supramolecule #1: Reconstitution of COPI-coated vesicles containing the cargo adapt...

SupramoleculeName: Reconstitution of COPI-coated vesicles containing the cargo adaptor protein GOLPH3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: Mus musculus COPI coatomer complex, recombinantly expressed in in...

SupramoleculeName: Mus musculus COPI coatomer complex, recombinantly expressed in insect cells and purified
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#7
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Homo sapiens GOLPH3, recombinantly expressed in E. coli and purified

SupramoleculeName: Homo sapiens GOLPH3, recombinantly expressed in E. coli and purified
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Homo sapiens Arf1, recombinantly expressed in E. coli and purified

SupramoleculeName: Homo sapiens Arf1, recombinantly expressed in E. coli and purified
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Golgi phosphoprotein 3

MacromoleculeName: Golgi phosphoprotein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.859555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSLTQRSSG LVQRRTEASR NAADKERAAG GGAGSSEDDA QSRRDEQDDD DKGDSKETRL TLMEEVLLLG LKDREGYTSF WNDCISSGL RGCMLIELAL RGRLQLEACG MRRKSLLTRK VICKSDAPTG DVLLDEALKH VKETQPPETV QNWIELLSGE T WNPLKLHY ...String:
MTSLTQRSSG LVQRRTEASR NAADKERAAG GGAGSSEDDA QSRRDEQDDD DKGDSKETRL TLMEEVLLLG LKDREGYTSF WNDCISSGL RGCMLIELAL RGRLQLEACG MRRKSLLTRK VICKSDAPTG DVLLDEALKH VKETQPPETV QNWIELLSGE T WNPLKLHY QLRNVRERLA KNLVEKGVLT TEKQNFLLFD MTTHPLTNNN IKQRLIKKVQ EAVLDKWVND PHRMDRRLLA LI YLAHASD VLENAFAPLL DEQYDLATKR VRQLLDLDPE VECLKANTNE VLWAVVAAFT K

UniProtKB: Golgi phosphoprotein 3

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Macromolecule #2: Coatomer subunit alpha

MacromoleculeName: Coatomer subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 138.617672 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLTKFETKSA RVKGLSFHPK RPWILTSLHN GVIQLWDYRM CTLIDKFDEH DGPVRGIDFH KQQPLFVSGG DDYKIKVWNY KLRRCLFTL LGHLDYIRTT FFHHEYPWIL SASDDQTIRV WNWQSRTCVC VLTGHNHYVM CAQFHPSEDL VVSASLDQTV R VWDISGLR ...String:
MLTKFETKSA RVKGLSFHPK RPWILTSLHN GVIQLWDYRM CTLIDKFDEH DGPVRGIDFH KQQPLFVSGG DDYKIKVWNY KLRRCLFTL LGHLDYIRTT FFHHEYPWIL SASDDQTIRV WNWQSRTCVC VLTGHNHYVM CAQFHPSEDL VVSASLDQTV R VWDISGLR KKNLSPGAVE SDVRGITGVD LFGTTDAVVK HVLEGHDRGV NWAAFHPTMP LIVSGADDRQ VKIWRMNESK AW EVDTCRG HYNNVSCAVF HPRQELILSN SEDKSIRVWD MSKRTGVQTF RRDHDRFWVL AAHPNLNLFA AGHDGGMIVF KLE RERPAY AVHGNMLHYV KDRFLRQLDF NSSKDVAVMQ LRSGSKFPVF NMSYNPAENA VLLCTRASNL ENSTYDLYTI PKDA DSQNP DAPEGKRSSG LTAVWVARNR FAVLDRMHSL LIKNLKNEIT KKIQVPNCDE IFYAGTGNLL LRDADSITLF DVQQK RTLA SVKISKVKYV IWSADMSHVA LLAKHAIVIC NRKLDALCNI HENIRVKSGA WDESGVFIYT TSNHIKYAVT TGDHGI IRT LDLPIYVTRV KGNNVYCLDR ECRPRVLTID PTEFKFKLAL INRKYDEVLH MVRNAKLVGQ SIIAYLQKKG YPEVALH FV KDEKTRFSLA LECGNIEIAL EAAKALDDKN CWEKLGEVAL LQGNHQIVEM CYQRTKNFDK LSFLYLITGN LEKLRKMM K IAEIRKDMSG HYQNALYLGD VSERVRILKN CGQKSLAYLS AATHGLDEEA ESLKETFDPE KETIPDIDPN AKLLQPPAP IMPLDTNWPL LTVSKGFFEG SIASKGKGGA LAADIDIDTV GTEGWGEDAE LQLDEDGFVE APEGLGEDVL GKGQEEGGGW DVEEDLELP PELDVPSGVS GSAEDGFFVP PTKGTSPTQI WCNNSQLPVD HILAGSFETA MRLLHDQVGV IQFGPYKQLF L QTYARGRT TYQALPCLPS MYSYPNRNWK DAGLKNGVPA VGLKLNDLIQ RLQLCYQLTT VGKFEEAVEK FRSILLSVPL LV VDNKQEI AEAQQLITIC REYIVGLCME IERKKLPKET LDQQKRICEM AAYFTHSNLQ PVHMILVLRT ALNLFFKLKN FKT AATFAR RLLELGPKPE VAQQTRKILS ACEKNPTDAC QLNYDMHNPF DICAASYRPI YRGKPVEKCP LSGACYSPEF KGQI CRVTT VTEIGKDVIG LRISPLQFR

UniProtKB: Coatomer subunit alpha

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Macromolecule #3: Coatomer subunit beta'

MacromoleculeName: Coatomer subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 102.566078 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPLRLDIKRK LTARSDRVKS VDLHPTEPWM LASLYNGSVC VWNHETQTLV KTFEVCDLPV RAAKFVARKN WVVTGADDMQ IRVFNYNTL ERVHMFEAHS DYIRCIAVHP TQPFILTSSD DMLIKLWDWD KKWSCSQVFE GHTHYVMQIV INPKDNNQFA S ASLDRTIK ...String:
MPLRLDIKRK LTARSDRVKS VDLHPTEPWM LASLYNGSVC VWNHETQTLV KTFEVCDLPV RAAKFVARKN WVVTGADDMQ IRVFNYNTL ERVHMFEAHS DYIRCIAVHP TQPFILTSSD DMLIKLWDWD KKWSCSQVFE GHTHYVMQIV INPKDNNQFA S ASLDRTIK VWQLGSSSPN FTLEGHEKGV NCIDYYSGGD KPYLISGADD RLVKIWDYQN KTCVQTLEGH AQNVSCASFH PE LPIIITG SEDGTVRIWH SSTYRLESTL NYGMERVWCV ASLRGSNNVA LGYDEGSIIV KLGREEPAMS MDANGKIIWA KHS EVQQAN LKAMGDTEIK DGERLPLAVK DMGSCEIYPQ TIQHNPNGRF VVVCGDGEYI IYTAMALRNK SFGSAQEFAW AHDS SEYAI RESNSIVKIF KNFKEKKSFK PDFGAESIYG GFLLGVRSVN GLAFYDWENT ELIRRIEIQP KHIFWSDSGE LVCIA TEES FFILKYLSEK VLAAQETHEG VTEDGIEDAF EVLGEIQEIV KTGLWVGDCF IYTSSVNRLN YYVGGEIVTI AHLDRT MYL LGYIPKDNRL YLGDKELNIV SYSLLVSVLE YQTAVMRRDF SMADKVLPTI PKEQRTRVAH FLEKQGFKQQ ALTVSTD PE HRFELALQLG ELKIAYQLAV EAESEQKWKQ LAELAISKCQ FSLAQECLHH AQDYGGLLLL ATASGNASMV NKLAEGAE R DGKNNVAFMS YFLQGKLDAC LELLIRTGRL PEAAFLARTY LPSQVSRVVK LWRENLSKVN QKAAESLADP TEYENLFPG LKEAFVVEEW VKETHADLWP AKQYPLVTPN EERNVMEEAK GFQPSRPTAQ QEPDGKPASS PVIMASQTTH KEEKSLLELE VDLDNLELE DIDTTDINLD EDILDD

UniProtKB: Coatomer subunit beta'

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Macromolecule #4: Coatomer subunit beta

MacromoleculeName: Coatomer subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 107.197961 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTAAENVCYT LINVPMDSEP PSEISLKNDL EKGDVKSKTE ALKKVIIMIL NGEKLPGLLM TIIRFVLPLQ DHTIKKLLLV FWEIVPKTT PDGRLLHEMI LVCDAYRKDL QHPNEFIRGS TLRFLCKLKE AELLEPLMPA IRACLEHRHS YVRRNAVLAI Y TIYRNFEH ...String:
MTAAENVCYT LINVPMDSEP PSEISLKNDL EKGDVKSKTE ALKKVIIMIL NGEKLPGLLM TIIRFVLPLQ DHTIKKLLLV FWEIVPKTT PDGRLLHEMI LVCDAYRKDL QHPNEFIRGS TLRFLCKLKE AELLEPLMPA IRACLEHRHS YVRRNAVLAI Y TIYRNFEH LIPDAPELIH DFLVNEKDAS CKRNAFMMLI HADQDRALDY LSTCIDQVQT FGDILQLVIV ELIYKVCHAN PS ERARFIR CIYNLLQSSS PAVKYEAAGT LVTLSSAPTA IKAAAQCYID LIIKESDNNV KLIVLDRLVE LKEHPAHERV LQD LVMDIL RVLSTPDLEV RKKTLQLALD LVSSRNVEEL VIVLKKEVIK TNNVSEHEDT DKYRQLLVRT LHSCSVRFPD MAAN VIPVL MEFLSDSNEA AAADVLEFVR EAIQRFDNLR MLIVEKMLEV FHAIKSVKIY RGALWILGEY CSTKEDIQSV MTEVR RSLG EIPIVESEIK KEAGELKPEE EITVGPVQKL VTEMGTYATQ SALSSSRPTK KEEDRPPLRG FLLDGDFFVA ASLATT LTK IALRYVALVQ EKKKQNSFVA EAMLLMATIL HLGKSSLPKK PITDDDVDRI SLCLKVLSEC SPLMNDIFNK ECRQSLS QM LSAKLEEEKL SQKKESEKRN VTVQPDDPIS FMQLTAKNEM NCKEDQFQLS LLAAMGNTQR KEAADPLASK LNKVTQLT G FSDPVYAEAY VHVNQYDIVL DVLVVNQTSD TLQNCTLELA TLGDLKLVEK PSPLTLAPHD FANIKANVKV ASTENGIIF GNIVYDVSGA ASDRNCVVLS DIHIDIMDYI QPATCTDAEF RQMWAEFEWE NKVTVNTNMT DLNDYLQHIL KSTNMKCLTP EKALSGYCG FMAANLYARS IFGEDALANV SIEKPVHQGP DAAVTGHIRI RAKSQGMALS LGDKINLSQK KTSL

UniProtKB: Coatomer subunit beta

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Macromolecule #5: Coatomer subunit delta

MacromoleculeName: Coatomer subunit delta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 57.30425 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVLLAAAVCT KAGKAIVSRQ FVEMTRTRIE GLLAAFPKLM NTGKQHTFVE TESVRYVYQP MEKLYMVLIT TKNSNILEDL ETLRLFSRV IPEYCRALEE NEISEHCFDL IFAFDEIVAL GYRENVNLAQ IRTFTEMDSH EEKVFRAVRE TQEREAKAEM R RKAKELQQ ...String:
MVLLAAAVCT KAGKAIVSRQ FVEMTRTRIE GLLAAFPKLM NTGKQHTFVE TESVRYVYQP MEKLYMVLIT TKNSNILEDL ETLRLFSRV IPEYCRALEE NEISEHCFDL IFAFDEIVAL GYRENVNLAQ IRTFTEMDSH EEKVFRAVRE TQEREAKAEM R RKAKELQQ ARRDAERQGK KAPGFGGFGS SAVSGGSTAA MITETIIETD KPKVAPAPAR PSGPSKALKL GAKGKEVDNF VD KLKSEGE TIMSSNMGKR TSEATKVHAP PINMESVHMK IEEKITLTCG RDGGLQNMEL HGMIMLRISD DKFGRIRLHV ENE DKKGVQ LQTHPNVDKK LFTAESLIGL KNPEKSFPVN SDVGVLKWRL QTTEESFIPL TINCWPSESG NGCDVNIEYE LQED NLELN DVVITIPLPS GVGAPVIGEI DGEYRHDSRR NTLEWCLPVI DAKNKSGSLE FSIPGQPNDF FPVQVSFISK KNYCN IQVT KVTQVDGNSP VRFSTETTFL VDKYEIL

UniProtKB: Coatomer subunit delta

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Macromolecule #6: Coatomer subunit gamma-1

MacromoleculeName: Coatomer subunit gamma-1 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 97.622703 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLKKFDKKDE ESGGGSNPLQ HLEKSAVLQE ARVFNETPIN PRKCAHILTK ILYLINQGEH LGTTEATEAF FAMTKLFQSN DPTLRRMCY LTIKEMSCIA EDVIIVTSSL TKDMTGKEDN YRGPAVRALC QITDSTMLQA VERYMKQAIV DKVPSVSSSA L VSSLHLLK ...String:
MLKKFDKKDE ESGGGSNPLQ HLEKSAVLQE ARVFNETPIN PRKCAHILTK ILYLINQGEH LGTTEATEAF FAMTKLFQSN DPTLRRMCY LTIKEMSCIA EDVIIVTSSL TKDMTGKEDN YRGPAVRALC QITDSTMLQA VERYMKQAIV DKVPSVSSSA L VSSLHLLK CSFDVVKRWV NEAQEAASSD NIMVQYHALG LLYHVRKNDR LAVSKMISKF TRHGLKSPFA YCMMIRVASK QL EEEDGSR DSPLFDFIES CLRNKHEMVV YEAASAIVNL PGCSAKELAP AVSVLQLFCS SPKAALRYAA VRTLNKVAMK HPS AVTACN LDLENLVTDS NRSIATLAIT TLLKTGSESS IDRLMKQISS FMSEISDEFK VVVVQAISAL CQKYPRKHAV LMNF LFTML REEGGFEYKR AIVDCIISII EENSESKETG LSHLCEFIED CEFTVLATRI LHLLGQEGPK TNNPSKYIRF IYNRV VLEH EEVRAGAVSA LAKFGAQNEE MLPSILVLLK RCVMDDDNEV RDRATFYLNV LEQKQKALNA GYILNGLTVS IPGLEK ALQ QYTLEPSEKP FDLKSVPLAT TPMAEQRPES TATAAVKQPE KVAATRQEIF QEQLAAVPEF QGLGPLFKSS PEPVALT ES ETEYVIRCTK HTFSDHLVFQ FDCTNTLNDQ TLENVTVQME PTEAYEVLSY VPARSLPYNQ PGTCYTLVAL PTEDPTAV A CTFSCVMKFT VKDCDPNTGE IDEEGYEDEY VLEDLEVTVA DHIQKVMKVN FEAAWDEVGD EFEKEETFTL STIKTLEEA VGNIVKFLGM HPCERSDKVP ENKNTHTLLL AGVFRGGHDI LVRSRLLLLD TVTMQVTARS SEELPVDIIL ASVG

UniProtKB: Coatomer subunit gamma-1

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Macromolecule #7: Coatomer subunit zeta-1

MacromoleculeName: Coatomer subunit zeta-1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.218168 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MEALILEPSL YTVKAILILD NDGDRLFAKY YDDTYPSVKE QKAFEKNIFN KTHRTDSEIA LLEGLTVVYK SSIDLYFYVI GSSYENELM LMAVLNCLFD SLSQMLRKNV EKRALLENME GLFLAVDEIV DGGVILESDP QQVVHRVALR GEDVPLTEQT V SQVLQSAK EQIKWSLLR

UniProtKB: Coatomer subunit zeta-1

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Macromolecule #8: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.721742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGNIFANLFK GLFGKKEMRI LMVGLDAAGK TTILYKLKLG EIVTTIPTIG FNVETVEYKN ISFTVWDVGG QDKIRPLWRH YFQNTQGLI FVVDSNDRER VNEAREELMR MLAEDELRDA VLLVFANKQD LPNAMNAAEI TDKLGLHSLR HRNWYIQATC A TSGDGLYE GLDWLSNQLR NQK

UniProtKB: ADP-ribosylation factor 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
125.0 mMKAcPotassium acetate
2.5 mMMgCl2Magnesium chloride
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: LEICA EM CPC
DetailsBudded and budding COPI vesicles were reconstituted by mixing liposomes with purified COPI coat protein, Arf1, GTPgammaS, and GOLPH3.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1 / Average electron dose: 3.114 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v3.0) / Number subtomograms used: 108432
ExtractionNumber tomograms: 206 / Number images used: 193104 / Reference model: EMDB-2985 / Software - Name: subTOM (ver. v1.1.5) / Software - details: https://github.com/DustinMorado/subTOM
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- ...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).
CTF correctionSoftware - Name: NOVACTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. v3.0)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

cie6

residue_range: 1-824, source_name: AlphaFold, initial_model_type: in silico model

5029

residue_range: 1-838, source_name: AlphaFold, initial_model_type: in silico model

jif7

residue_range: 1-710, source_name: AlphaFold, initial_model_type: in silico model1-499; 536-710

xj75

residue_range: 1-247, source_name: AlphaFold, initial_model_type: in silico model1-177; 224-247

qze5

residue_range: 1-582, source_name: AlphaFold, initial_model_type: in silico model

1924

residue_range: 6-150, source_name: AlphaFold, initial_model_type: in silico model

4077

residue_range: 15-181, source_name: AlphaFold, initial_model_type: in silico model

h4a6

residue_range: 10-290, source_name: AlphaFold, initial_model_type: in silico model10-25; 55-298
RefinementProtocol: RIGID BODY FIT / Overall B value: 200
Output model

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

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