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Yorodumi- EMDB-22778: Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 po... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22778 | |||||||||
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Title | Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class without Sec62 | |||||||||
Map data | unsharpened, lowpass-filtered map | |||||||||
Sample |
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Keywords | Sec61 / translocon / endoplasmic reticulum / protein translocation / Sec62 / Sec63 / channel / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information misfolded protein transport / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein transmembrane import into intracellular organelle / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity ...misfolded protein transport / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein transmembrane import into intracellular organelle / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity / filamentous growth / post-translational protein targeting to endoplasmic reticulum membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / peptide transmembrane transporter activity / 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 / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Itskanov S / Park E | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Authors: Samuel Itskanov / Katie M Kuo / James C Gumbart / Eunyong Park / Abstract: Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their ...Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. In the present study, we determined cryo-electron microscopy (cryo-EM) structures of several variants of Sec61-Sec62-Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and luminal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational 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_22778.map.gz | 32.2 MB | EMDB map data format | |
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Header (meta data) | emd-22778-v30.xml emd-22778.xml | 24.5 KB 24.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22778_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_22778.png | 33.3 KB | ||
Masks | emd_22778_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-22778.cif.gz | 7.2 KB | ||
Others | emd_22778_additional_1.map.gz emd_22778_half_map_1.map.gz emd_22778_half_map_2.map.gz | 59.4 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22778 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22778 | HTTPS FTP |
-Related structure data
Related structure data | 7kaoMC 7kahC 7kaiC 7kajC 7kakC 7kalC 7kamC 7kanC 7kapC 7kaqC 7karC 7kasC 7katC 7kauC 7kb5C 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_22778.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened, lowpass-filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22778_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map
File | emd_22778_additional_1.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-volume 1
File | emd_22778_half_map_1.map | ||||||||||||
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Annotation | half-volume 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-volume 2
File | emd_22778_half_map_2.map | ||||||||||||
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Annotation | half-volume 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Endoplasmic reticulum protein-transport machinery Sec complex fro...
Entire | Name: Endoplasmic reticulum protein-transport machinery Sec complex from yeast with Sec61 pore ring mutated. |
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Components |
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-Supramolecule #1: Endoplasmic reticulum protein-transport machinery Sec complex fro...
Supramolecule | Name: Endoplasmic reticulum protein-transport machinery Sec complex from yeast with Sec61 pore ring mutated. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Sec61 has the following mutations: M90L/T185I/M294I/M450L |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / 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: 52.936086 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSSNRVLDLF KPFESFLPEV IAPERKVPYN QKLIWTGVSL LIFLILGQIP LYGIVSSETS DPLYWLRAML ASNRGTLLEL GVSPIITSS LIFQFLQGTQ LLQIRPESKQ DRELFQIAQK VCAIILILGQ ALVVVMTGNY GAPSDLGLPI CLLLIFQLMF A SLIVMLLD ...String: MSSNRVLDLF KPFESFLPEV IAPERKVPYN QKLIWTGVSL LIFLILGQIP LYGIVSSETS DPLYWLRAML ASNRGTLLEL GVSPIITSS LIFQFLQGTQ LLQIRPESKQ DRELFQIAQK VCAIILILGQ ALVVVMTGNY GAPSDLGLPI CLLLIFQLMF A SLIVMLLD ELLSKGYGLG SGISLFIATN IAEQIFWRAF APTTVNSGRG KEFEGAVIAF FHLLAVRKDK KRALVEAFYR TN LPNMFQV LMTVAIFLFV LYLQGFRYEL PIRSTKVRGQ IGIYPIKLFY TSNTPIILQS ALTSNIFLIS QILFQKYPTN PLI RLIGVW GIRPGTQGPQ MALSGLAYYI QPLMSLSEAL LDPIKTIVYI TFVLGSCAVF SKTWIEISGT SPRDIAKQFK DQGM VINGK RETSIYRELK KIIPTAAAFG GATIGALSVG SDLLGTLGSG ASILLATTTI 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: 75.301062 KDa |
Sequence | String: PTNYEYDEAS ETWPSFILTG LLMVVGPMTL LQIYQIFFGA NAEDGNSGKS KEFNEEVFKN LNEEYTSDEI KQFRRKFDKN SNKKSKIWS RRNIIIIVGW ILVAILLQRI NSNDAIKDAA TKLFDPYEIL GISTSASDRD IKSAYRKLSV KFHPDKLAKG L TPDEKSVM ...String: PTNYEYDEAS ETWPSFILTG LLMVVGPMTL LQIYQIFFGA NAEDGNSGKS KEFNEEVFKN LNEEYTSDEI KQFRRKFDKN SNKKSKIWS RRNIIIIVGW ILVAILLQRI NSNDAIKDAA TKLFDPYEIL GISTSASDRD IKSAYRKLSV KFHPDKLAKG L TPDEKSVM EETYVQITKA YESLTDELVR QNYLKYGHPD GPQSTSHGIA LPRFLVDGSA SPLLVVCYVA LLGLILPYFV SR WWARTQS YTKKGIHNVT ASNFVSNLVN YKPSEIVTTD LILHWLSFAH EFKQFFPDLQ PTDFEKLLQD HINRRDSGKL NNA KFRIVA KCHSLLHGLL DIACGFRNLD IALGAINTFK CIVQAVPLTP NCQILQLPNV DKEHFITKTG DIHTLGKLFT LEDA KIGEV LGIKDQAKLN ETLRVASHIP NLKIIKADFL VPGENQVTPS STPYISLKVL VRSAKQPLIP TSLIPEENLT EPQDF ESQR DPFAMMSKQP LVPYSFAPFF PTKRRGSWCC LVSSQKDGKI LQTPIIIEKL SYKNLNDDKD FFDKRIKMDL TKHEKF DIN DWEIGTIKIP LGQPAPETVG DFFFRVIVKS TDYFTTDLDI TMNMKVRDSP AVEQVEVYSE EDDEYSTDDD ETESDDE SD ASDYTDIDTD TEAEDDESPE 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: GLOW DISCHARGE / Pretreatment - Time: 35 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 43478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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) / Average electron dose: 48.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |