[English] 日本語
![](img/lk-miru.gif)
- EMDB-22783: Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 po... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-22783 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3 double mutant, class without Sec62 | |||||||||
![]() | Unsharpened, lowpass-filtered map | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Itskanov S / Park E | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 32.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 24.6 KB 24.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.3 KB | Display | ![]() |
Images | ![]() | 31.3 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() ![]() | 59.4 MB 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7katMC ![]() 7kahC ![]() 7kaiC ![]() 7kajC ![]() 7kakC ![]() 7kalC ![]() 7kamC ![]() 7kanC ![]() 7kaoC ![]() 7kapC ![]() 7kaqC ![]() 7karC ![]() 7kasC ![]() 7kauC ![]() 7kb5C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened, lowpass-filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened map
File | emd_22783_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_22783_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_22783_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Endoplasmic reticulum protein-transport machinery Sec complex fro...
Entire | Name: Endoplasmic reticulum protein-transport machinery Sec complex from yeast![]() |
---|---|
Components |
|
-Supramolecule #1: Endoplasmic reticulum protein-transport machinery Sec complex fro...
Supramolecule | Name: Endoplasmic reticulum protein-transport machinery Sec complex from yeast type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Sec63 has the following mutations: E440R/F481S/del(441-447) Sec61 has the following mutations: M90L/T185I/M294I/M450L |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Protein transport protein SEC61
Macromolecule | Name: Protein transport protein SEC61 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 52.936086 KDa |
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: ![]() |
-Macromolecule #2: Protein transport protein SSS1
Macromolecule | Name: Protein transport protein SSS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 8.958641 KDa |
Sequence | String: MARASEKGEE KKQSNNQVEK LVEAPVEFVR EGTQFLAKCK KPDLKEYTKI VKAVGIGFIA VGIIGYAIKL IHIPIRYVIV UniProtKB: ![]() |
-Macromolecule #3: Protein transport protein SBH1
Macromolecule | Name: Protein transport protein SBH1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 8.723155 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MSSPTPPGGQ RTLQKRKQGS SQKVAASAPK KNTNSNNSIL KIYSDEATGL RVDPLVVLFL AVGFIFSVVA LHVISKVAGK LF UniProtKB: ![]() |
-Macromolecule #4: Protein translocation protein SEC63
Macromolecule | Name: Protein translocation protein SEC63 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 76.312039 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GGSGGSGGSG GSGGSPTNYE YDEASETWPS FILTGLLMVV GPMTLLQIYQ IFFGANAEDG NSGKSKEFNE EVFKNLNEEY TSDEIKQFR RKFDKNSNKK SKIWSRRNII IIVGWILVAI LLQRINSNDA IKDAATKLFD PYEILGISTS ASDRDIKSAY R KLSVKFHP ...String: GGSGGSGGSG GSGGSPTNYE YDEASETWPS FILTGLLMVV GPMTLLQIYQ IFFGANAEDG NSGKSKEFNE EVFKNLNEEY TSDEIKQFR RKFDKNSNKK SKIWSRRNII IIVGWILVAI LLQRINSNDA IKDAATKLFD PYEILGISTS ASDRDIKSAY R KLSVKFHP DKLAKGLTPD EKSVMEETYV QITKAYESLT DELVRQNYLK YGHPDGPQST SHGIALPRFL VDGSASPLLV VC YVALLGL ILPYFVSRWW ARTQSYTKKG IHNVTASNFV SNLVNYKPSE IVTTDLILHW LSFAHEFKQF FPDLQPTDFE KLL QDHINR RDSGKLNNAK FRIVAKCHSL LHGLLDIACG FRNLDIALGA INTFKCIVQA VPLTPNCQIL QLPNVDKEHF ITKT GDIHT LGKLFTLEDA KIGEVLGIKD QAKLNETLRV ASHIPNLKII KADFLVPGRP YISLKVLVRS AKQPLIPTSL IPEEN LTEP QDSESQRDPF AMMSKQPLVP YSFAPFFPTK RRGSWCCLVS SQKDGKILQT PIIIEKLSYK NLNDDKDFFD KRIKMD LTK HEKFDINDWE IGTIKIPLGQ PAPETVGDFF FRVIVKSTDY FTTDLDITMN MKVRDSPAVE QVEVYSEEDD EYSTDDD ET ESDDESDASD YTDIDTDTEA EDDESPEGEN LYFQ UniProtKB: ![]() |
-Macromolecule #5: Translocation protein SEC66
Macromolecule | Name: Translocation protein SEC66 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
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 | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Concentration | 5 mg/mL |
---|---|
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 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 42017 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 K3 (6k x 4k) / Average electron dose: 48.5 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |