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- EMDB-16017: Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. -

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Basic information

Entry
Database: EMDB / ID: EMD-16017
TitleMolecular view of ER membrane remodeling by the Sec61/TRAP translocon.
Map data
Sample
  • Complex: Mammlian Ribosome Sec61 TRAP complex
    • Protein or peptide: x 16 types
    • RNA: x 2 types
  • Protein or peptide: x 1 types
KeywordsMembrane protein / protein translocation / protein biogenesis. / TRANSPORT PROTEIN
Function / homology
Function and homology information


ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein transmembrane transporter activity / protein targeting / MDM2/MDM4 family protein binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / cytosolic large ribosomal subunit ...ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein transmembrane transporter activity / protein targeting / MDM2/MDM4 family protein binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / synapse / endoplasmic reticulum membrane / RNA binding / metal ion binding
Similarity search - Function
Translocon-associated protein beta (TRAPB) / Translocon-associated / Translocon-associated protein subunit beta / Translocon-associated protein subunit gamma / Translocon-associated protein, delta subunit precursor (TRAP-delta) / Translocon-associated protein, gamma subunit (TRAP-gamma) / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Protein secE/sec61-gamma signature. / SecE/Sec61-gamma subunits of protein translocation complex ...Translocon-associated protein beta (TRAPB) / Translocon-associated / Translocon-associated protein subunit beta / Translocon-associated protein subunit gamma / Translocon-associated protein, delta subunit precursor (TRAP-delta) / Translocon-associated protein, gamma subunit (TRAP-gamma) / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Protein secE/sec61-gamma signature. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / Ribosomal protein L23 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L23, N-terminal domain / Ribosomal protein L31e, conserved site / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / 60S ribosomal protein L19 / Ribosomal protein L37e, conserved site / Ribosomal protein L37e / Ribosomal protein L31e / Ribosomal protein L37ae/L37e / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L37e / Ribosomal protein L31e signature. / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L37e signature. / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L22 signature. / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L24 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Translation protein SH3-like domain superfamily / Zinc-binding ribosomal protein / Ribosomal protein L23/L15e core domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Ribosomal protein L23/L25 N-terminal domain-containing protein / Large ribosomal subunit protein uL29 / Uncharacterized protein / RL26 protein / Protein transport protein Sec61 subunit gamma / Translocon-associated protein subunit gamma / Ribosomal protein L37 / Translocon-associated protein subunit beta / Translocon-associated protein subunit delta / Ribosomal protein L19 ...Ribosomal protein L23/L25 N-terminal domain-containing protein / Large ribosomal subunit protein uL29 / Uncharacterized protein / RL26 protein / Protein transport protein Sec61 subunit gamma / Translocon-associated protein subunit gamma / Ribosomal protein L37 / Translocon-associated protein subunit beta / Translocon-associated protein subunit delta / Ribosomal protein L19 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL22
Similarity search - Component
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsKarki S / Javanainen M / Tranter D / Rehan S / Huiskonen J / Happonen L / Paavilainen V
Funding support Finland, 2 items
OrganizationGrant numberCountry
Academy of Finland338836 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: EMBO Rep / Year: 2023
Title: Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.
Authors: Sudeep Karki / Matti Javanainen / Shahid Rehan / Dale Tranter / Juho Kellosalo / Juha T Huiskonen / Lotta Happonen / Ville Paavilainen /
Abstract: Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates ...Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.
History
DepositionOct 24, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16017.png

Downloads & links

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Map

FileDownload / File: emd_16017.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 800 pix.
= 664. Å		0.83 Å/pix.
x 800 pix.
= 664. Å		0.83 Å/pix.
x 800 pix.
= 664. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.00275
Minimum - Maximum-1.5345773 - 3.3123946
Average (Standard dev.)0.0023221828 (±0.046807267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 664.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16017_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_16017_half_map_2.map
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Sample components

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Entire : Mammlian Ribosome Sec61 TRAP complex

EntireName: Mammlian Ribosome Sec61 TRAP complex
Components
  • Complex: Mammlian Ribosome Sec61 TRAP complex
    • Protein or peptide: Translocon-associated protein subunit alpha
    • Protein or peptide: Translocon-associated protein subunit beta
    • Protein or peptide: Translocon-associated protein subunit delta
    • Protein or peptide: Translocon-associated protein subunit gamma
    • RNA: RNA (1766)
    • RNA: RNA (156-MER)
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Ribosomal protein L19
    • Protein or peptide: RL22 protein (Fragment)
    • Protein or peptide: Ribosomal protein L23/L25 N-terminal domain-containing proteinRibosome
    • Protein or peptide: RL26 protein (Fragment)
    • Protein or peptide: Sec61b
    • Protein or peptide: Large ribosomal subunit protein eL31
    • Protein or peptide: Protein transport protein Sec61 subunit gammaProtein targeting
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: Ribosomal protein L37
    • Protein or peptide: Large ribosomal subunit protein eL38
    • Protein or peptide: 60S ribosomal protein L39
  • Protein or peptide: Sec61a

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Supramolecule #1: Mammlian Ribosome Sec61 TRAP complex

SupramoleculeName: Mammlian Ribosome Sec61 TRAP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#6, #1-#2, #7-#11, #13-#19 / Details: Mammlian ribosome-Sec61 TRAP complex
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 3.2 MDa

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Macromolecule #1: RNA (1766)

MacromoleculeName: RNA (1766) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 1.1865795 MDa
SequenceString: CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC ...String:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC GCUCCCCGGC GCCGCUCGUG GGGGGCCCAA GUCCUUCUGA UCGAGGCCCA GCCCGUGGAC GGUGUGAGGC CG GUAGCGG CCCCCGGCGC GCCGGGCCCG GGUCUUCCCG GAGUCGGGUU GCUUGGGAAU GCAGCCCAAA GCGGGUGGUA AAC UCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAAGGGA AAGUUGAAAA GAACUUUGAA GAGA GAGUU CAAGAGGGCG UGAAACCGUU AAGAGGUAAA CGGGUGGGGU CCGCGCAGUC CGCCCGGAGG AUUCAACCCG GCGGC GGGU CCGGCCGUGU CGGCGGCCCG GCGGAUCUUU CCCGCGCGGG GGACCGUCCC CCGACCGGCG ACCGGCCGCC GCCGGG CGC AUUUCCACCG CGGCGGUGCG CCGCGACCGG CUCCGGGACG GCUGGGAAGG CCCGGCGGGG AAGGUGGCUC GGCCGAG UG UUACAGCCCC CCCGGCAGCA GCACUCGCCG AAUCCCGGGG CCGAGGGAGC GAGACCCGUC GCCGCGCUCU CCCCCCUC C CGGCGCCGCC GGGGGGGGCC GGGCCACCCC UCCCACGGCG CGACCGCUCG GGGCGGACUG UCCCCAGUGC GCCCCGGGC GGGUCGCGCC GUCGGGCCCG GGGGAGGGGC CACGCGCGCG UCCCCCGAAG AGGGGGACGG CGGAGCGAGC GCACGGGGUC GGCGGCGAC GUCGGCUACC CACCCGACCC GUCUUGAAAC ACGGACCAAG GAGUCUAACA CGUGCGCGAG UCGGGGGCUC G CACGAAAG CCGCCGUGGC GCAAUGAAGG UGAAGGCCGG CGCGCUCGCC GGCCGAGGUG GGAUCCCGAG GCCUCUCCAG UC CGCCGAG GGCGCACCAC CGGCCCGUCU CGCCCGCCGC GCCGGGGAGG UGGAGCACGA GCGCACGUGU UAGGACCCGA AAG AUGGUG AACUAUGCCU GGGCAGGGCG AAGCCAGAGG AAACUCUGGU GGAGGUCCGU AGCGGUCCUG ACGUGCAAAU CGGU CGUCC GACCUGGGUA UAGGGGCGAA AGACUAAUCG AACCAUCUAG UAGCUGGUUC CCUCCGAAGU UUCCCUCAGG AUAGC UGGC GCUCUCGCAC ACGCAGUUUU AUCCGGUAAA GCGAAUGAUU AGAGGUCUUG GGGCCGAAAC GAUCUCAACC UAUUCU CAA ACUUUAAAUG GGUAAGAAGC CCGGCUCGCU GGCGUGAGCC GGGCGUGGAA UGGAGUGCCU AGUGGGCCAC UUUUGGU AA GCAGAACUGG CGCUGCGGGA UGAACCGAAC GCCGGGUUAA GGCGCCCGAU GCCGACGCUC AUCAGACCCC AGAAAAGG U GUUGGUUGAU AUAGACAGCA GGACGGUGGC CAUGGAAGUC GGAAUCCGCU AAGGAGUGUG UAACAACUCA CCUGCCGAA UCAACUAGCC CUGAAAAUGG AUGGCGCUGG AGCGUCGGGC CCAUACCCGG CCGUCGCCGG CAGUCGAGAG UGGACGGGAG CGGCGGGGG CGGCGCGCGC GCGCGCCCGC CCCCGGAGCC CCGCGGACGC UACGCCGCGA CGAGUAGGAG GGCCGCUGCG G UGAGCCUU GAAGCCUAGG GCGCGGGCCC GGGUGGAGCC GCCGCAGGUG CAGAUCUUGG UGGUAGUAGC AAAUAUUCAA AC GAGAACU UUGAAGGCCG AAGUGGAGAA GGGUUCCAUG UGAACAGCAG UUGAACAUGG GUCAGUCGGU CCUGAGAGAU GGG CGAGCG CCGUUCCGAA GGGACGGGCG AUGGCCUCCG UUGCCCUCGG CCGAUCGAAA GGGAGUCGGG UUCAGAUCCC CGAA UCCGG AGUGGCGGAG AUGGGCGCCG CGAGGCGUCC AGUGCGGUAA CGCGACCGAU CCCGGAGAAG CCGGCGGGAG CCCCG GGGA GAGUUCUCUU UUCUUUGUGA AGGGCAGGGC GCCCUGGAAU GGGUUCGCCC CGAGAGAGGG GCCCGUGCCU UGGAAA GCG UCGCGGUUCC GGCGGCGUCC GGUGAGCUCU CGCUGGCCCU UGAAAAUCCG GGGGAGAGGG UGUAAAUCUC GCGCCGG GC CGUACCCAUA UCCGCAGCAG GUCUCCAAGG UGAACAGCCU CUGGCAUGUU GGAACAAUGU AGGUAAGGGA AGUCGGCA A GCCGGAUCCG UAACUUCGGG AUAAGGAUUG GCUCUAAGGG CUGGGUCGGU CGUCGGCCGG CGCCUAGCAG CCGACUUAG AACUGGUGCG GACCAGGGGA AUCCGACUGU UUAAUUAAAA CAAAGCAUCG CGAAGGCCCG CGGCGGGUGU UGACGCGAUG UGAUUUCUG CCCAGUGCUC UGAAUGUCAA AGUGAAGAAA UUCAAUGAAG CGCGGGUAAA CGGCGGGAGU AACUAUGACU C UCUUAAGG UAGCCAAAUG CCUCGUCAUC UAAUUAGUGA CGCGCAUGAA UGGAUGAACG AGAUUCCCAC UGUCCCUACC UA CUAUCCA GCGAAACCAC AGCCAAGGGA ACGGGCUUGG CGGAAUCAGC GGGGAAAGAA GACCCUGUUG AGCUUGACUC UAG UCUGGC ACGGUGAAGA GACAUGUUUU UUCACUGACC CGGUGAGGCG GGGGGGCGAG CCCCGAGGGG CUCUCGCUUC UGGC GCCAA GCGCCCGGCC GCGCGCCGGC CGGGCGCGAC CCGCUCCGGG GACAGUGCCA GGUGGGGAGU UUGACUGGGG CGGUA CACC UGUCAAACGG UAACGCAGGU GUCCUAAGGC GAGCUCAGGG AGGACAGAAA CCUCCCGUGG AGCAGAAGGG CAAAAG CUC GCUUGAUCUU GAUUUUCAGU ACGAAUACAG ACCGUGAAAG CGGGGCCUCA CGAUCCUUCU GACCUUUUGG GUUUUAA GC AGGAGGUGUC AGAAAAGUUA CCACAGGGAU AACUGGCUUG UGGCGGCCAA GCGUUCAUAG CGACGUCGCU UUUUGAUC C UUCGAUGUCG GCUCUUCCUA UCAUUGUGAA GCAGAAUUCA CCAAGCGUUG GAUUGUUCAC CCACUAAUAG GGAACGUGA GCUGGGUUUA GACCGUCGUG AGACAGGUUA GUUUUACCCU ACUGAUGAUG UGUUGUUGCC AUGGUAAUCC UGCUCAGUAC GAGAGGAAC CGCAGGUUCA GACAUUUGGU GUAUGUGCUU GGCUGAGGAG CCAAUGGGGC GAAGCUACCA UCUGUGGGAU U AUGACUGA ACGCCUCUAA GUCAGAAUCC CGCCCAGGCG GAACGAUACG GCAGCGCCGC GGAGCCUCGG UUGGCCUCGG AU AGCCGGU CCCCCGCGGG GUCCGGUGCG GAGUGCCCUU CGUCCUGGGA AACGGGGCGC GGCCGGAGAG GCGGCCGCCC CCU CGCCCG UCACGCACGC CGUUCGUGGG GAACCUGGCG CUAAACCAUU CGUAGACGAC CUGCUUCUGG GUCGGGGUUU CGUA CGUAG CAGAGCAGCU CCCUCGCUGC GAUCUAUUGA AAGUCAGCCC UCGACACAAG GGUUUGU

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Macromolecule #2: RNA (156-MER)

MacromoleculeName: RNA (156-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 50.143648 KDa
SequenceString:
CGACUCUUAG CGGUGGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGA CACAUUGAU CAUCGACACU UCGAACGCAC UUGCGGCCCC GGGUUCCUCC CGGGGCUACG CCUGUCUGAG CGUCGCU

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Macromolecule #3: Translocon-associated protein subunit alpha

MacromoleculeName: Translocon-associated protein subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 39.38143 KDa
SequenceString: MRSLRRLLLL LLLVFPATLL LRGSPGGSLA VAQDLTEDEE TVEDSIIEDE DDEAEVEEDE PTDLAEDKEE DGVSGEPEAS PSADTTILF VKGEDFPANN IVKFLVGFTN KGTEDFIVES LDASFRYPQD YQFYIQNFTA LPLNTVVPPQ RQATFEYSFI P AEPMGGRP ...String:
MRSLRRLLLL LLLVFPATLL LRGSPGGSLA VAQDLTEDEE TVEDSIIEDE DDEAEVEEDE PTDLAEDKEE DGVSGEPEAS PSADTTILF VKGEDFPANN IVKFLVGFTN KGTEDFIVES LDASFRYPQD YQFYIQNFTA LPLNTVVPPQ RQATFEYSFI P AEPMGGRP FGLVINLNYK DLNGNVFQDA VFNQTVTIIE REDGLDGETI FMYMFLAGLG LLVVVGLHQL LESRKRKRPI QK VEMGTSS QNDVDMSWIP QETLNQIMQS RRVVSGLLKK HYKSSMTSFF KVKTFTSPAG STSPTLHELL VFTCYSRQFL HSH CCTPAA PMSVFTDGSC GTRFCSLSSR ALGVCLW

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Macromolecule #4: Translocon-associated protein subunit beta

MacromoleculeName: Translocon-associated protein subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 20.478418 KDa
SequenceString:
MCTMRLLAFA VLALFAVTQA EEGARLLASK SLLNRYAVEG RDLTLQYNIY NVGSSAALDV ELSDDSFPPE DFGIVSGMLN VKWDRIAPA SNVSHTVVLR PLKAGYFNFT SATVTYLAQE DGPVVIGFTS APGQGGILAQ REFDRRFSPH FLDWAAFGVM T LPSIGVPL LLWYSSKRKY DTPKTKKN

UniProtKB: Translocon-associated protein subunit beta

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Macromolecule #5: Translocon-associated protein subunit delta

MacromoleculeName: Translocon-associated protein subunit delta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 18.901377 KDa
SequenceString:
MAALASLGAL ALLLLSGLSC CSAEACVEPQ ITPSYYTTSD AVISTETVFI VEISLTCKNR VQNMALYADV SGKQFPVTRG QDVGRYQVS WSLDHKSAHA GTYEVRFFDE ESYSLLRKAQ RNNEDVSVIP PLFTVSVDHR GTWNGPWVST EVLAAAIGLV I YYLAFSAK SHIQA

UniProtKB: Translocon-associated protein subunit delta

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Macromolecule #6: Translocon-associated protein subunit gamma

MacromoleculeName: Translocon-associated protein subunit gamma / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 21.100504 KDa
SequenceString:
MAPKGGPKQQ SEEDLLLQDF SRNLSAKSSA LFFGNAFIVS AIPIWLYWRI WHMDLIQSAV LYSVMTLVST YLVAFAYKNV KFVLKHKVA QKREDAVSKE VTRKLSEADN RKMSRKEKDE RILWKKNEVA DYEATTFSIF YNNTLFLVLV IVASFFILKN F NPTVNYIL SISASSGLIA LLSTGSK

UniProtKB: Translocon-associated protein subunit gamma

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Macromolecule #7: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 21.414129 KDa
SequenceString:
MVRYSLDPEN PTKSCKSRGS NLRVHFKNTR ETAQAIKGMH IRKATKYLKD VTLKKQCVPF RRYNGGVGRC AQAKQWGWTQ GRWPKKSAE FLLHMLKNAE SNAELKGLDV DSLVIEHIQV NKAPKMRRRT YRAHGRINPY MSSPCHIEMI LTEKEQIVPK P EEEVAQKK KISQKKLKKQ KLTARE

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #8: Ribosomal protein L19

MacromoleculeName: Ribosomal protein L19 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 23.535281 KDa
SequenceString: MSMLRLQKRL ASSVLRCGKK KVWLDPNETN EIANANSRQQ IRKLIKDGLI IRKPVTVHSR ARCRKNTLAR RKGRHMGIGK RKGTANARM PEKVTWMRRM RILRRLLRRY RESKKIDRHM YHSLYLKVKG NVFKNKRILM EHIHKLKADK ARKKLLADQA E ARRSKTKE ...String:
MSMLRLQKRL ASSVLRCGKK KVWLDPNETN EIANANSRQQ IRKLIKDGLI IRKPVTVHSR ARCRKNTLAR RKGRHMGIGK RKGTANARM PEKVTWMRRM RILRRLLRRY RESKKIDRHM YHSLYLKVKG NVFKNKRILM EHIHKLKADK ARKKLLADQA E ARRSKTKE ARKRREERLQ AKKEEIIKTL SKEEETKK

UniProtKB: Ribosomal protein L19

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Macromolecule #9: RL22 protein (Fragment)

MacromoleculeName: RL22 protein (Fragment) / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 14.784962 KDa
SequenceString:
MAPVKKLVAK GGKKKKQVLK FTLDCTHPVE DGIMDAANFE QFLQERIKVN GKAGNLGGGV VTIERSKSKI TVTSEVPFSK RYLKYLTKK YLKKNNLRDW LRVVANSKES YELRYFQINQ DEEEEEDED

UniProtKB: Uncharacterized protein

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Macromolecule #10: Ribosomal protein L23/L25 N-terminal domain-containing protein

MacromoleculeName: Ribosomal protein L23/L25 N-terminal domain-containing protein
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 17.740193 KDa
SequenceString:
MAPKAKKEAP APPKAEAKAK ALKAKKAVLK GVHSHKKKKI RTSPTFRRPK TLRLRRQPKY PRKSAPRRNK LDHYAIIKFP LTTESAMKK IEDNNTLVFI VDVKANKHQI KQAVKKLYDI DVAKVNTLIR PDGEKKAYVR LAPDYDALDV ANKIGII

UniProtKB: Ribosomal protein L23/L25 N-terminal domain-containing protein

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Macromolecule #11: RL26 protein (Fragment)

MacromoleculeName: RL26 protein (Fragment) / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 15.891787 KDa
SequenceString:
MKFNPFVTSD RSKNRKRHFN APSHIRRKIM SSPLSKELRQ KYNVRSMPIR KDDEVQVVRG HYKGQQIGKV VQVYRKKYVI YIERVQREK ANGTTVHVGI HPSKVVITRL KLDKDRKKIL ERKAKSRQVG KEKGK

UniProtKB: RL26 protein

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Macromolecule #12: Sec61a

MacromoleculeName: Sec61a / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 52.034062 KDa
SequenceString: MGIKFLEVIK PFCVILPEIQ KPERKIQFKE KVLWTAITLF IFLVCCQIPL FGIMSSDSAD PYWMRVILAS NRGTLMALGI SPIVTSGLI MQLLAGAKII EVGDTPKDRA LFNGAQKLFG MTITIGQSIV YVMTGMYGDP SEMGAGVCLL ITIQLFVAGL I VLLLDELL ...String:
MGIKFLEVIK PFCVILPEIQ KPERKIQFKE KVLWTAITLF IFLVCCQIPL FGIMSSDSAD PYWMRVILAS NRGTLMALGI SPIVTSGLI MQLLAGAKII EVGDTPKDRA LFNGAQKLFG MTITIGQSIV YVMTGMYGDP SEMGAGVCLL ITIQLFVAGL I VLLLDELL QKGYGLGSGI SLFIATNICE TIVWKAFSPT TVNTGRGMEF EGAIIALFHL LATRTDKVRA LREAFYRQNL PN LMNLIAT IFVFAVVIYF QGFRVDLPIK SARYRGQYNT YPIKLFYTSN IPIILQSALV SNLYVISQML SARFSGNLLV SLL GTWSDT SSGGPARAYP VGGLCHYLSP PESFGSVLED PVHAVVYIVF MLGSCAFFSK TWIEVSGSSA KDVAKQLKEQ QMVM RGHRE TSMVHELNRY IPTAAAFGGL CIGALSVLAD FLGAIGSGTG ILLAVTIIYQ YFEIFVKEQS EVGSMGALLF

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Macromolecule #13: Sec61b

MacromoleculeName: Sec61b / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 2.486056 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #14: Large ribosomal subunit protein eL31

MacromoleculeName: Large ribosomal subunit protein eL31 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 14.494938 KDa
SequenceString:
MAPAKKGGEK KKGRSAINEV VTREYTINIH KRIHGVGFKK RAPRALKEIR KFAMKEMGTP DVRIDTRLNK AVWAKGIRNV PYRIRVRLS RKRNEDEDSP NKLYTLVTYV PVTTFKNLQT VNVDEN

UniProtKB: Large ribosomal subunit protein eL31

+
Macromolecule #15: Protein transport protein Sec61 subunit gamma

MacromoleculeName: Protein transport protein Sec61 subunit gamma / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 9.352173 KDa
SequenceString:
MEDGDIMDQV MQFVEPSRQF VKDSIRLVKR CTKPDRKEFQ KIAMATAIGF AIMGFIGFFV KLIHIPINNI IVYLLNFSGK K

UniProtKB: Protein transport protein Sec61 subunit gamma

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Macromolecule #16: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 14.591649 KDa
SequenceString:
MAKIKARDLR GKKKEELLKQ LEDLKVELSQ LRVAKVTGGA ASKLSKIRVV RKSIARVLTV INQTQKENLR KFYKGKKYKP LDLRPKKTR AMRRRLNKHE ENLKTKKQQR KERLYPLRKF AVKA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #17: Ribosomal protein L37

MacromoleculeName: Ribosomal protein L37 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 11.111032 KDa
SequenceString:
MTKGTSSFGK RRNKTHTLCR RCGSKAYHLQ KSTCGKCGYP AKRKRKYNWS AKAKRRNTTG TGRMRHLKIV YRRFRHGFRE GTTPKPKRA AVAASSSS

UniProtKB: Ribosomal protein L37

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Macromolecule #18: Large ribosomal subunit protein eL38

MacromoleculeName: Large ribosomal subunit protein eL38 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 8.238948 KDa
SequenceString:
MPRKIEEIKD FLLTARRKDA KSVKIKKNKD NVKFKVRCSR YLYTLVITDK EKAEKLKQSL PPGLAVKELK

+
Macromolecule #19: 60S ribosomal protein L39

MacromoleculeName: 60S ribosomal protein L39 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 6.426759 KDa
SequenceString:
MSSHKTFRIK RFLAKKQKQN RPIPQWIRMK TGNKIRYNSK RRHWRRTKLG L

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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

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMHepesHepes
300.0 mMKoAcPotassium acetate
10.0 mMMgAcMagnesium acetate
1.0 mMDDTDithiothritol
0.003 percentLMNGLauryl maltose neopentyl glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA PLUNGER
DetailsPurified Ribosome Sec61/TRAP complex

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 30294 / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1098031
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61177

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-8bf9:
Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.

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