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Yorodumi- EMDB-28204: CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28204 | |||||||||
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Title | CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1 | |||||||||
Map data | Half map B | |||||||||
Sample |
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Keywords | Tether / SNARE / Complex / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information Golgi to ER transport vesicle membrane / vesicle fusion with endoplasmic reticulum / ER-dependent peroxisome organization / RZZ complex / Dsl1/NZR complex / COPI-dependent Golgi-to-ER retrograde traffic / regulation of ER to Golgi vesicle-mediated transport / SNARE complex / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...Golgi to ER transport vesicle membrane / vesicle fusion with endoplasmic reticulum / ER-dependent peroxisome organization / RZZ complex / Dsl1/NZR complex / COPI-dependent Golgi-to-ER retrograde traffic / regulation of ER to Golgi vesicle-mediated transport / SNARE complex / SNAP receptor activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / mitotic spindle assembly checkpoint signaling / cytoplasmic side of endoplasmic reticulum membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / autophagy / protein transport / nuclear envelope / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | DAmico KA / Jeffrey PD / Hughson FM | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure of a membrane tethering complex incorporating multiple SNAREs. Authors: Kevin A DAmico / Abigail E Stanton / Jaden D Shirkey / Sophie M Travis / Philip D Jeffrey / Frederick M Hughson / Abstract: Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial ...Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial attachment of two membranes. Complementary SNAREs then form membrane-bridging complexes whose assembly draws the membranes together for fusion. Here we present a cryo-electron microscopy structure of the simplest known MTC, the 255-kDa Dsl1 complex of Saccharomyces cerevisiae, bound to the two SNAREs that anchor it to the endoplasmic reticulum. N-terminal domains of the SNAREs form an integral part of the structure, stabilizing a Dsl1 complex configuration with unexpected similarities to the 850-kDa exocyst MTC. The structure of the SNARE-anchored Dsl1 complex and its comparison with exocyst reveal what are likely to be common principles underlying MTC function. Our structure also implies that tethers and SNAREs can work together as a single integrated machine. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28204.map.gz | 200 MB | EMDB map data format | |
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Header (meta data) | emd-28204-v30.xml emd-28204.xml | 27.2 KB 27.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28204_fsc.xml emd_28204_fsc_2.xml emd_28204_fsc_3.xml emd_28204_fsc_4.xml | 13.4 KB 13.4 KB 13.4 KB 13.3 KB | Display Display Display Display | FSC data file |
Images | emd_28204.png | 57.4 KB | ||
Filedesc metadata | emd-28204.cif.gz | 8.3 KB | ||
Others | emd_28204_half_map_1.map.gz emd_28204_half_map_2.map.gz | 198.5 MB 198.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28204 | HTTPS FTP |
-Validation report
Summary document | emd_28204_validation.pdf.gz | 986.3 KB | Display | EMDB validaton report |
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Full document | emd_28204_full_validation.pdf.gz | 985.8 KB | Display | |
Data in XML | emd_28204_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_28204_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28204 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28204 | HTTPS FTP |
-Related structure data
Related structure data | 8ekiMC 8ftuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28204.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Half map B | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.114 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_28204_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_28204_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dsl1 complex bound to SNARE proteins Sec20 and Use1
Entire | Name: Dsl1 complex bound to SNARE proteins Sec20 and Use1 |
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Components |
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-Supramolecule #1: Dsl1 complex bound to SNARE proteins Sec20 and Use1
Supramolecule | Name: Dsl1 complex bound to SNARE proteins Sec20 and Use1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508/S288c |
Molecular weight | Theoretical: 255.41261 KDa |
-Supramolecule #2: Dsl1 Complex
Supramolecule | Name: Dsl1 Complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#5 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508/S288c |
-Macromolecule #1: Protein transport protein SEC20
Macromolecule | Name: Protein transport protein SEC20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 32.244254 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MVVTFLQDLE VLQDALLNNL QKLSAISRRK ESGESKHDNK DSFAAIANEH NDEEEEIEFE DLVNIIESKV SDFESVLKCS IVEMTYKYP ELKLQWEKSP RYDQCDKLHI VKLDKQMNED IYAQLVEELD FVLQFVDWFY CYRLKVKEIL RQHHKRDLAW N DEKRDRAI ...String: MVVTFLQDLE VLQDALLNNL QKLSAISRRK ESGESKHDNK DSFAAIANEH NDEEEEIEFE DLVNIIESKV SDFESVLKCS IVEMTYKYP ELKLQWEKSP RYDQCDKLHI VKLDKQMNED IYAQLVEELD FVLQFVDWFY CYRLKVKEIL RQHHKRDLAW N DEKRDRAI KFHAVDYDKL HQGTSSSSSL TSTSMEKAST REKLLSKTKQ LTNNLVRGNQ ILQSGILQSD LNLDELRAQT NS LTQIDDK YTQFETVFKK TADLVKVLEN ASHQEKRD UniProtKB: Protein transport protein SEC20 |
-Macromolecule #2: Protein transport protein USE1
Macromolecule | Name: Protein transport protein USE1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 24.254781 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MAETSNDPFL SYVLSSKQLT NLNRLRRKAV TKQLGSSDDN KVSEEFLRYQ HTYQREAFEY LQTKHDAHKI MESQYEQYQS SSKTRRYSI DLDSVDAVDT ESQTEYPNEE FIDRNEDSEA VMELRKRLLG KGQNKGLGYE TTKSVDRQIE DQDTLQQDLI Q DMSKLVGS ...String: MAETSNDPFL SYVLSSKQLT NLNRLRRKAV TKQLGSSDDN KVSEEFLRYQ HTYQREAFEY LQTKHDAHKI MESQYEQYQS SSKTRRYSI DLDSVDAVDT ESQTEYPNEE FIDRNEDSEA VMELRKRLLG KGQNKGLGYE TTKSVDRQIE DQDTLQQDLI Q DMSKLVGS LKQGAVAFQS ALDEDKQVLG AAEIGIQVAS QGLMDVSGKL RKYD UniProtKB: Protein transport protein USE1 |
-Macromolecule #3: Protein transport protein TIP20
Macromolecule | Name: Protein transport protein TIP20 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 81.253062 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MNGIDDLLNI NDRIKQVQNE RNELASKLQN LKQSLASNDT EVALSEVIAQ DIIEVGASVE GLEQLRAKYG DLQILNKLEK VAVQQTQMQ AGVDKLDSFE RQLDELAEQP PDQFTLDDVK ALHSKLTSVF ATVPQINNID SQYAAYNKLK SKVTGKYNDV I IQRLATNW ...String: MNGIDDLLNI NDRIKQVQNE RNELASKLQN LKQSLASNDT EVALSEVIAQ DIIEVGASVE GLEQLRAKYG DLQILNKLEK VAVQQTQMQ AGVDKLDSFE RQLDELAEQP PDQFTLDDVK ALHSKLTSVF ATVPQINNID SQYAAYNKLK SKVTGKYNDV I IQRLATNW SNTFDQKLLE AQWDTQKFAS TSVGLVKCLR ENSTKLYQLS LLYLPLEEET QNGDSERPLS RSNNNQEPVL WN FKSLANN FNVRFTYHFH ATSSSSKIET YFQFLNDYLA ENLYKCINIF HDDCNGLTKP VIHEQFINYV LQPIRDKVRS TLF QNDLKT LIVLISQILA TDKNLLNSFH YHGLGLVSLI SDEVWEKWIN YEVEMANRQF INITKNPEDF PKSSQNFVKL INKI YDYLE PFYDLDFDLL VRYKLMTCSL IFMNLTSSYL DYILTVDSLN ETRTKEQELY QTMAKLQHVN FVYRKIKSLS SNFIF IQLT DIVNSTESKK YNSLFQNVEN DYEKAMSTDM QNSIVHRIQK LLKETLRNYF KISTWSTLEM SVDENIGPSS VPSAEL VNS INVLRRLINK LDSMDIPLAI SLKVKNELLN VIVNYFTESI LKLNKFNQNG LNQFLHDFKS LSSILSLPSH ATNYKCM SL HELVKILKLK YDPNNQQFLN PEYIKTGNFT SLKEAYSIKY LKDTKIQDAL YRIIYGNIL UniProtKB: Protein transport protein TIP20 |
-Macromolecule #4: Protein transport protein SEC39
Macromolecule | Name: Protein transport protein SEC39 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 82.483797 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MLEEQLYLLA CIFASRADTR NIKKLSTRLG SQSKYLEILC VLWPELDDPK NLLFLRELEE EVQSPEGEET TDEDVIVELL ESDSSLIPL IESDTTTRSN RYHELQEFIS KKLNNKTLEN FEEWLRERIL ICNEMIPETP LLYSVLWETA KSKVLSTKFI G WVEGVLKP ...String: MLEEQLYLLA CIFASRADTR NIKKLSTRLG SQSKYLEILC VLWPELDDPK NLLFLRELEE EVQSPEGEET TDEDVIVELL ESDSSLIPL IESDTTTRSN RYHELQEFIS KKLNNKTLEN FEEWLRERIL ICNEMIPETP LLYSVLWETA KSKVLSTKFI G WVEGVLKP LDHLNKRLHL IFKINEWEKM PDSELFKIIF DGVEDMQGYI GIADVIEDEL APTLSYGKKW ETFITEFFNK QQ FSLKSDT NYQLFIKLYY SLEKGVKDNS EASRKLQSNV VDILFHNSEN LFNLSSLTHK LDELWSILSG FPDEITIEEQ KTI TALEMK QFMEFFIKCS TKFSFKEIFA ITQEEESAQL AHFSSLCHEE FNKANEISSF LQAMYETVLD ISKDDKIFTR ISMD EKLYS ILEILLQMNE FAYIEAIIER FDYSNNTQIY ELLVKFFWHF FNNASNGLRK EPEMKKASQT LQIIQKHMSQ RAGTN LTKL EVLLEISDKL SHYSINLNKS HNGARDTAFK PSNILEYRDC PLDIISNLLE LNPRLYKDLP TTKSLLFGIY DSLSIN REG QTGKVEVDLM VLHIDYALVN LDFGTAYELG KQVFEICQEA GQHMMKALGD EHWLTFYQMG KFVDPNWVDN EIPTEII VL QMSILGRLLE VCPLEEVEIV TSQWSTLELE LSARDLVKDK YALDGQNDNK SKVGGIAREI FHNVTNF UniProtKB: Protein transport protein SEC39 |
-Macromolecule #5: Protein transport protein DSL1
Macromolecule | Name: Protein transport protein DSL1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 91.445133 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MKHHHHHHHG AAGTSLYKKA GENLYFQGSM ESLFPNKGEI IRELLKDPLI LKNDSKRSNG SELELDSSDL LQREAILANE LNILDNLKT FLNLIKEVKT NLNILELENC YYSLQSLRKK MRNNAAYLKQ SFNFQQSIST YVDTLHLELV STLYKILTNG F WKITENSI ...String: MKHHHHHHHG AAGTSLYKKA GENLYFQGSM ESLFPNKGEI IRELLKDPLI LKNDSKRSNG SELELDSSDL LQREAILANE LNILDNLKT FLNLIKEVKT NLNILELENC YYSLQSLRKK MRNNAAYLKQ SFNFQQSIST YVDTLHLELV STLYKILTNG F WKITENSI QFTPTVEWGK DKVHIEYDTF MDFVAQQYFP KGSLDNQAWF ILDMTSADSQ EQVRAKLNTI MKEYMNLSRI VS MIKNSIF ISGKEISYEN EKNILVFSKS SSHGQHCVST VLTSFEAVCD FMLDGLAFRD RKTLSYELGP LFNTEFTKFV KNN ASIILE SLDSPLKNLV SVINNKLTRL VAKSEVTNWT HSGKEIQDLL MNKQLYYNLL LDKVLESHIS EIRSIFEDPK KSWQ NLEVV ELTTSNTNTM SEKIGKNDSD VQNEKELHNA VSKDDDWNWE VEDDDADAWG DEIDVNIDDE EEKTNQEKEK EPEEE ENAW DEAWAIDENI DDASLENGKE HLKAHDVGSL DKDHIEVTQL PKLFLAISQN FKSSFADSHV DEQYFAYKYN LLQTSY MAM CTANFSHNWC QLYVDMRYLI ERDEKLYRIK ELTRNLLETK LNMKYRIVCQ LIRHQLTEFR ENERNPSWDA TIEKLLP YI LKEIVRPLQK IRGEEGSRYL LSFLNFLYND CVTKEILKWQ IISEVNSENL GELVSLLVNN TDIQLLAKEP SYKKMREK F ATMGKFLPLH LKEIMEMFYN GDFYLFATDE LIQWIELLFA DTPLRRNAID DIYEIRGTAL DD UniProtKB: Protein transport protein DSL1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Buffer was made fresh from concentrated components and sterile filtered. NP40 was not present during protein purification but was an additive during the grid preparation. | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Force=0 Wait Time=0 Blot Time=6s Drain Time=0. | |||||||||||||||
Details | Sample was consistently in the thickest regions of ice only, often close to the edges of the carbon hole |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 5857 / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |