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- EMDB-22777: Cryo-EM structure of the Sec complex from T. lanuginosus, Sec62 a... -

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Basic information

Entry
Database: EMDB / ID: EMD-22777
TitleCryo-EM structure of the Sec complex from T. lanuginosus, Sec62 anchor domain mutant (delta anchor)
Map dataUnsharpened, lowpass-filtered map
Sample
  • Complex: Endoplasmic reticulum protein-transport machinery Sec complex from T. lanuginosus
    • Protein or peptide: Protein transport channel Sec61 complex, alpha subunit (Sec61)
    • Protein or peptide: Protein transport channel Sec61 complex, beta subunit (Sbh1)
    • Protein or peptide: Protein transport channel Sec61 complex, gamma subunit (Sss1)
    • Protein or peptide: Protein transport protein Sec63
    • Protein or peptide: Protein transport protein Sec66/Sec71
    • Protein or peptide: Protein transport protein Sec72
    • Protein or peptide: Protein transport protein Sec62
Function / homology
Function and homology information


misfolded protein transport / Sec62/Sec63 complex / translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cytosol to endoplasmic reticulum transport / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cytosol to endoplasmic reticulum transport / 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 / signal sequence binding / post-translational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane, translocation / peptide transmembrane transporter activity / nuclear inner membrane / retrograde protein transport, ER to cytosol / protein transmembrane transporter activity / ERAD pathway / guanyl-nucleotide exchange factor activity / cell periphery / ribosome binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / RNA binding / membrane / cytosol
Similarity search - Function
Translocation protein Sec66 / Preprotein translocase subunit Sec66 / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Nt-dnaJ domain signature. ...Translocation protein Sec66 / Preprotein translocase subunit Sec66 / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Nt-dnaJ domain signature. / DnaJ domain, conserved site / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / DnaJ domain / Sec63 domain / Sec63 Brl domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Protein translocation protein SEC63 / Protein transport protein SEC61 / Translocation protein SEC66 / Protein transport protein SSS1 / Translocation protein SEC72 / Protein transport protein SBH1
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsItskanov S / Park E
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: 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
DepositionOct 1, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.195
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.195
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22777.png

Downloads & links

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Map

FileDownload / File: emd_22777.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened, lowpass-filtered map
Voxel sizeX=Y=Z: 1.19 Å
Density
Contour LevelBy AUTHOR: 0.195 / Movie #1: 0.195
Minimum - Maximum-0.1455447 - 0.48766953
Average (Standard dev.)0.0019717852 (±0.02539129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.191.191.19
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z304.640304.640304.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ410410410
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1460.4880.002

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Supplemental data

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Mask #1

Fileemd_22777_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_22777_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 1

Fileemd_22777_half_map_1.map
Annotationhalf-volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 2

Fileemd_22777_half_map_2.map
Annotationhalf-volume 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Endoplasmic reticulum protein-transport machinery Sec complex fro...

EntireName: Endoplasmic reticulum protein-transport machinery Sec complex from T. lanuginosus
Components
  • Complex: Endoplasmic reticulum protein-transport machinery Sec complex from T. lanuginosus
    • Protein or peptide: Protein transport channel Sec61 complex, alpha subunit (Sec61)
    • Protein or peptide: Protein transport channel Sec61 complex, beta subunit (Sbh1)
    • Protein or peptide: Protein transport channel Sec61 complex, gamma subunit (Sss1)
    • Protein or peptide: Protein transport protein Sec63
    • Protein or peptide: Protein transport protein Sec66/Sec71
    • Protein or peptide: Protein transport protein Sec72
    • Protein or peptide: Protein transport protein Sec62

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Supramolecule #1: Endoplasmic reticulum protein-transport machinery Sec complex fro...

SupramoleculeName: Endoplasmic reticulum protein-transport machinery Sec complex from T. lanuginosus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Anchor domain of Sec62 (residues 319-338) is replaced with the linker GGSGGSGGS
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Protein transport channel Sec61 complex, alpha subunit (Sec61)

MacromoleculeName: Protein transport channel Sec61 complex, alpha subunit (Sec61)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MSGLRFLDLI KPFTPLLPEV AAPETKVPFN QKLMWTGLTL LIFLVMSQMP LYGIVSSDTS DPLYWLRMM LASNRGTLME LGITPIISSG MVFQLLAGTH LIDVNLDLKT DRELYQTAQK L FAIILSFG QACVHVLTGL YGQPSDLGAG ICVLLIVQLV VAGLVVILLD ...String:
MSGLRFLDLI KPFTPLLPEV AAPETKVPFN QKLMWTGLTL LIFLVMSQMP LYGIVSSDTS DPLYWLRMM LASNRGTLME LGITPIISSG MVFQLLAGTH LIDVNLDLKT DRELYQTAQK L FAIILSFG QACVHVLTGL YGQPSDLGAG ICVLLIVQLV VAGLVVILLD ELLQKGYGLG SG ISLFIAT NICESIVWKA FSPTTINTGR GPEFEGAIIA LFHLLLTWPD KQRALREAFY RQS LPNIMN LLATLLVFAA VIYLQGFRVE IPVKSARQRG VRGSYPVRLF YTSNMPIMLQ SALC SNVFL ISQMLYSRFS DNLLVRLLGV WEPREGSAQL HAASGIAYYM SPPLNFKEAL LDPVH TVVY ITFMLVACAL FSKTWIEVSG SSPRDVAKQL KDQGLVMAGH REQSMYKELK RVIPTA AAF GGACIGALSV ASDLLGALGS GTGILLAVTI IYGYFEMAAR EGDFGQGLRG LVPGNGS

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Macromolecule #2: Protein transport channel Sec61 complex, beta subunit (Sbh1)

MacromoleculeName: Protein transport channel Sec61 complex, beta subunit (Sbh1)
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString:
MASSGAESGS ESKSPNPGAG SGPGSASGSS AGVIRPSSPT PPGGPRAAIR RRAAADHKES LRNARPSST RAAGAGGSSG TMLKLYTDES PGLRVDPVVV LVLSLCFIFS VVGLHVIAKI T RKFSS

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Macromolecule #3: Protein transport channel Sec61 complex, gamma subunit (Sss1)

MacromoleculeName: Protein transport channel Sec61 complex, gamma subunit (Sss1)
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString:
MSEQVQELLD IPRDFLKDGM QFIHKCQKPD RKEFKKVCQA VAIGFVAMGA IGYIVKLVHI PINNILVAG S

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Macromolecule #4: Protein transport protein Sec63

MacromoleculeName: Protein transport protein Sec63 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: GGSGGSGGSG GSGGSMSSRE YNYDENGQFF PFFVLTLTGL VTLPLTYSLL KPPKK VEST APRIKSDFKP QHDDIIQNQK RKRLRKERRV KRAIAVVVGW AIIGYMVYLI IVTRRT APK IWDPYEILGI SRSADERAIA RRYKRLSLLY HPDKVRPDPS KNETMEMLNQ ...String:
GGSGGSGGSG GSGGSMSSRE YNYDENGQFF PFFVLTLTGL VTLPLTYSLL KPPKK VEST APRIKSDFKP QHDDIIQNQK RKRLRKERRV KRAIAVVVGW AIIGYMVYLI IVTRRT APK IWDPYEILGI SRSADERAIA RRYKRLSLLY HPDKVRPDPS KNETMEMLNQ RFVELTK AY KALTDEEIRN NYLQYGHPDG KQSYSIGIAL PKLIIEEGSG KYVLMLYASL LGILLPYI V GRWWYGSQRY TREKVLAASA GNMFREYEGT MIGGPIVNAL STGEEYKEML SGPKAEEGL AKVEKKVLAL DEKILSAKDR EVLRKIDNPV RRKALALLWA YLNRIDLEDP VLNEEKYEAG SIALSLTES FTAIALAFGN LIPIIGAYRI SQCIVQAISP GSSPLLQLPY FTPKVVESVE G ADVKTHLS VQKYLDMPEE RRRSLTVGPG LLTEDQYNSA IAVAKQLPLF AISKAFFKVA GE RVVTPSS LVQLVIKGRI IPPGSTGVPD VTEKDLEDID PDEADVNAII GRKGATKPSG KSG DENDGD RVQPPLAHAP YLPRDHPPRW HIFLADAKQG KIAVPPFTFT TFDKPIFDEQ GKPT FNMQT LRMQFQAPPQ VGNFSFVLHM ISDSYMGFDV KQEITLQVED PSKAAVLQEE DDISE PDED SIAGQMQALK TGVPPKKKKV VESDDDESDT EGDEEDTSET DTETDTDEEG SGTGEN LYF Q

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Macromolecule #5: Protein transport protein Sec66/Sec71

MacromoleculeName: Protein transport protein Sec66/Sec71 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MDWLTLVVPF AYLGVLIGCL ATFSSLYRRR KAAKAASLEP WFPPHLQRDI YHSLLHLDQQ QQNEKKTRV PETVLKAALL RRAAEDIKRV MAIREQKQAL ALLLQRGSVG DELWQRFLRA E KEMEDEVR DVVAEANSYA PNWGQVIFQS AREMDANATY RARMEEYQAT ...String:
MDWLTLVVPF AYLGVLIGCL ATFSSLYRRR KAAKAASLEP WFPPHLQRDI YHSLLHLDQQ QQNEKKTRV PETVLKAALL RRAAEDIKRV MAIREQKQAL ALLLQRGSVG DELWQRFLRA E KEMEDEVR DVVAEANSYA PNWGQVIFQS AREMDANATY RARMEEYQAT VAEERAWWDK KR ASIQEGF MKELDAEKER PATAASTATN TTSTTSDDDA VLVEAEKEGT SSPAPGKKKK KGK KGS

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Macromolecule #6: Protein transport protein Sec72

MacromoleculeName: Protein transport protein Sec72 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MSSDLDTYTH YPLHLDPSSK AVSLATTEGQ TPAQTEAVEA ELQQLNALHR SLISLDPPNV PPPPLPINP KRSAQITKLK ETANTAYKRG NHGEAVRLYS YAIEMAAGRP GWEPVNLARE E LSGLYANR AQAHMAQQMW PEGWVDAKCS VESKPVGNAK GWWRGGKCLV ...String:
MSSDLDTYTH YPLHLDPSSK AVSLATTEGQ TPAQTEAVEA ELQQLNALHR SLISLDPPNV PPPPLPINP KRSAQITKLK ETANTAYKRG NHGEAVRLYS YAIEMAAGRP GWEPVNLARE E LSGLYANR AQAHMAQQMW PEGWVDAKCS VESKPVGNAK GWWRGGKCLV EMGRYDEARA WI EQALGIE GPASDGGKEL AALLEEIKAG SQRRQGS

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Macromolecule #7: Protein transport protein Sec62

MacromoleculeName: Protein transport protein Sec62 / type: protein_or_peptide / ID: 7
Details: T. lanuginosus Sec62 with residues 319-338 replaced with the linker GGSGGSGGS
Enantiomer: LEVO
Source (natural)Organism: Thermomyces lanuginosus (fungus)
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MAAPPPGMTP QQFAALQQHM QQQIAAEAAK RGMTVEEFSK MQREQLNAEA AKAGMTPEQY INQLRMRALQ QRAAMQQQMQ QQQQQGGQGQ TQGQGQGQGQ QGQGQPQVQH VQHVQQQVSV NPNAPPNPKA IALAKWLRSQ NLKARTCILD GQRREMFKVK RALRALESPE ...String:
MAAPPPGMTP QQFAALQQHM QQQIAAEAAK RGMTVEEFSK MQREQLNAEA AKAGMTPEQY INQLRMRALQ QRAAMQQQMQ QQQQQGGQGQ TQGQGQGQGQ QGQGQPQVQH VQHVQQQVSV NPNAPPNPKA IALAKWLRSQ NLKARTCILD GQRREMFKVK RALRALESPE YQKAAAKNKL LPPVTDRASA ENAFKLLPLS FLALRVSKVS SNYNKGKRVK GLWTVKVEQH QDTDPMTHYV WLYEGPQWKQ KALAAAFVIG IFAIVLFPLW PIMLRQGVWY LSVGMLGLLG LFFALAIVRL ILFCVTVFVV PPGGSGGSGG SKKKKPKKAK AAVSKSQEKG AAPTTAAPEA PTATTTSSEA QPSSSSGTAS KRNLAASVED AEEGS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 42017 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

Particle selectionNumber selected: 229825 / Details: autopicked particles
CTF correctionSoftware: (Name: Warp (ver. 1.0.7), cryoSPARC (ver. 2.12))
Startup modelType of model: OTHER / Details: Ab initio reconstruction from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Details: Non-uniform refinement from cryoSPARC / Number images used: 76726
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12) / Details: Non-uniform refinement from cryoSPARC
FSC plot (resolution estimation)

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