+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0336 | |||||||||
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Title | Cryo-EM structure of the yeast Sec complex | |||||||||
Map data | Sharpened full map | |||||||||
Sample |
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Keywords | Sec61 / Sec63 / Sec71 / Sec72 / Sec66 / protein translocation / translocon / endoplasmic reticulum / secretion / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information protein transmembrane import into intracellular organelle / misfolded protein transport / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity ...protein transmembrane import into intracellular organelle / misfolded protein transport / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity / post-translational protein targeting to endoplasmic reticulum membrane / filamentous growth / SRP-dependent cotranslational protein targeting to membrane, translocation / peptide transmembrane transporter activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / nuclear inner membrane / retrograde protein transport, ER to cytosol / protein transmembrane transporter activity / : / guanyl-nucleotide exchange factor activity / cell periphery / ribosome binding / structural molecule activity / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
Authors | Park E / Itskanov S | |||||||||
Citation | Journal: Science / Year: 2019 Title: Structure of the posttranslational Sec protein-translocation channel complex from yeast. Authors: Samuel Itskanov / Eunyong Park / Abstract: The Sec61 protein-conducting channel mediates transport of many proteins, such as secretory proteins, across the endoplasmic reticulum (ER) membrane during or after translation. Posttranslational ...The Sec61 protein-conducting channel mediates transport of many proteins, such as secretory proteins, across the endoplasmic reticulum (ER) membrane during or after translation. Posttranslational transport is enabled by two additional membrane proteins associated with the channel, Sec63 and Sec62, but its mechanism is poorly understood. We determined a structure of the Sec complex (Sec61-Sec63-Sec71-Sec72) from by cryo-electron microscopy (cryo-EM). The structure shows that Sec63 tightly associates with Sec61 through interactions in cytosolic, transmembrane, and ER-luminal domains, prying open Sec61's lateral gate and translocation pore and thus activating the channel for substrate engagement. Furthermore, Sec63 optimally positions binding sites for cytosolic and luminal chaperones in the complex to enable efficient polypeptide translocation. Our study provides mechanistic insights into eukaryotic posttranslational protein translocation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0336.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-0336-v30.xml emd-0336.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0336_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_0336.png | 58 KB | ||
Filedesc metadata | emd-0336.cif.gz | 6.7 KB | ||
Others | emd_0336_additional.map.gz | 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0336 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0336 | HTTPS FTP |
-Related structure data
Related structure data | 6n3qMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0336.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unfiltered full map
File | emd_0336_additional.map | ||||||||||||
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Annotation | Unfiltered full map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Posttranslational Sec protein-translocation channel complex
Entire | Name: Posttranslational Sec protein-translocation channel complex |
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Components |
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-Supramolecule #1: Posttranslational Sec protein-translocation channel complex
Supramolecule | Name: Posttranslational Sec protein-translocation channel complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
-Macromolecule #1: Protein transport protein SEC61
Macromolecule | Name: Protein transport protein SEC61 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 52.978148 KDa |
Sequence | String: MSSNRVLDLF KPFESFLPEV IAPERKVPYN QKLIWTGVSL LIFLILGQIP LYGIVSSETS DPLYWLRAML ASNRGTLLEL GVSPIITSS MIFQFLQGTQ LLQIRPESKQ DRELFQIAQK VCAIILILGQ ALVVVMTGNY GAPSDLGLPI CLLLIFQLMF A SLIVMLLD ...String: MSSNRVLDLF KPFESFLPEV IAPERKVPYN QKLIWTGVSL LIFLILGQIP LYGIVSSETS DPLYWLRAML ASNRGTLLEL GVSPIITSS MIFQFLQGTQ LLQIRPESKQ DRELFQIAQK VCAIILILGQ ALVVVMTGNY GAPSDLGLPI CLLLIFQLMF A SLIVMLLD ELLSKGYGLG SGISLFTATN IAEQIFWRAF APTTVNSGRG KEFEGAVIAF FHLLAVRKDK KRALVEAFYR TN LPNMFQV LMTVAIFLFV LYLQGFRYEL PIRSTKVRGQ IGIYPIKLFY TSNTPIMLQS ALTSNIFLIS QILFQKYPTN PLI RLIGVW GIRPGTQGPQ MALSGLAYYI QPLMSLSEAL LDPIKTIVYI TFVLGSCAVF SKTWIEISGT SPRDIAKQFK DQGM VINGK RETSIYRELK KIIPTAAAFG GATIGALSVG SDLLGTLGSG ASILMATTTI YGYYEAAAKE GGFTKNLVPG FSDLM UniProtKB: Protein transport protein SEC61 |
-Macromolecule #2: Protein transport protein SSS1
Macromolecule | Name: Protein transport protein SSS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 8.958641 KDa |
Sequence | String: MARASEKGEE KKQSNNQVEK LVEAPVEFVR EGTQFLAKCK KPDLKEYTKI VKAVGIGFIA VGIIGYAIKL IHIPIRYVIV UniProtKB: Protein transport protein SSS1 |
-Macromolecule #3: Protein transport protein SBH1
Macromolecule | Name: Protein transport protein SBH1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 8.723155 KDa |
Sequence | String: MSSPTPPGGQ RTLQKRKQGS SQKVAASAPK KNTNSNNSIL KIYSDEATGL RVDPLVVLFL AVGFIFSVVA LHVISKVAGK LF UniProtKB: Protein transport protein SBH1 |
-Macromolecule #4: Protein translocation protein SEC63
Macromolecule | Name: Protein translocation protein SEC63 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 75.432258 KDa |
Sequence | String: MPTNYEYDEA SETWPSFILT GLLMVVGPMT LLQIYQIFFG ANAEDGNSGK SKEFNEEVFK NLNEEYTSDE IKQFRRKFDK NSNKKSKIW SRRNIIIIVG WILVAILLQR INSNDAIKDA ATKLFDPYEI LGISTSASDR DIKSAYRKLS VKFHPDKLAK G LTPDEKSV ...String: MPTNYEYDEA SETWPSFILT GLLMVVGPMT LLQIYQIFFG ANAEDGNSGK SKEFNEEVFK NLNEEYTSDE IKQFRRKFDK NSNKKSKIW SRRNIIIIVG WILVAILLQR INSNDAIKDA ATKLFDPYEI LGISTSASDR DIKSAYRKLS VKFHPDKLAK G LTPDEKSV MEETYVQITK AYESLTDELV RQNYLKYGHP DGPQSTSHGI ALPRFLVDGS ASPLLVVCYV ALLGLILPYF VS RWWARTQ SYTKKGIHNV TASNFVSNLV NYKPSEIVTT DLILHWLSFA HEFKQFFPDL QPTDFEKLLQ DHINRRDSGK LNN AKFRIV AKCHSLLHGL LDIACGFRNL DIALGAINTF KCIVQAVPLT PNCQILQLPN VDKEHFITKT GDIHTLGKLF TLED AKIGE VLGIKDQAKL NETLRVASHI PNLKIIKADF LVPGENQVTP SSTPYISLKV LVRSAKQPLI PTSLIPEENL TEPQD FESQ RDPFAMMSKQ PLVPYSFAPF FPTKRRGSWC CLVSSQKDGK ILQTPIIIEK LSYKNLNDDK DFFDKRIKMD LTKHEK FDI NDWEIGTIKI PLGQPAPETV GDFFFRVIVK STDYFTTDLD ITMNMKVRDS PAVEQVEVYS EEDDEYSTDD DETESDD ES DASDYTDIDT DTEAEDDESP E UniProtKB: Protein translocation protein SEC63 |
-Macromolecule #5: Translocation protein SEC66
Macromolecule | Name: Translocation protein SEC66 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 24.263939 KDa |
Sequence | String: MSEFNETKFS NNGTFFETEE PIVETKSISV YTPLIYVFIL VVSLVMFASS YRKKQAKKIS EQPSIFDEND AHDLYFQIKE MSENEKIHE KVLKAALLNR GAESVRRSLK LKELAPQINL LYKNGSIGED YWKRFETEVK LIELEFKDTL QEAERLQPGW V QLFVMVCK ...String: MSEFNETKFS NNGTFFETEE PIVETKSISV YTPLIYVFIL VVSLVMFASS YRKKQAKKIS EQPSIFDEND AHDLYFQIKE MSENEKIHE KVLKAALLNR GAESVRRSLK LKELAPQINL LYKNGSIGED YWKRFETEVK LIELEFKDTL QEAERLQPGW V QLFVMVCK EICFNQALSR RYQSILKRKE VCIKEWELKI NNDGRLVN UniProtKB: Translocation protein SEC66 |
-Macromolecule #6: Translocation protein SEC72
Macromolecule | Name: Translocation protein SEC72 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 21.63109 KDa |
Sequence | String: MVTLEYNANS KLITASDAVV ALSTETNIDQ INVLTTSLIG ETNPNFTPQP NEALSKMIKG LFESGMKNLQ QKKLNEALKN VSLAIEMAQ RKRAPWEAFA IQLPELHFML RSKIDLCLIL GKHLEALQDL DFLLGTGLIQ PDVFVRKADC LLKLRQWEEA R ATCERGLA ...String: MVTLEYNANS KLITASDAVV ALSTETNIDQ INVLTTSLIG ETNPNFTPQP NEALSKMIKG LFESGMKNLQ QKKLNEALKN VSLAIEMAQ RKRAPWEAFA IQLPELHFML RSKIDLCLIL GKHLEALQDL DFLLGTGLIQ PDVFVRKADC LLKLRQWEEA R ATCERGLA LAPEDMKLRA LLIETARNLA EYNGE UniProtKB: Translocation protein SEC72 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 43103 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |