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

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Basic information

Entry
Database: PDB / ID: 8bf9
TitleMolecular view of ER membrane remodeling by the Sec61/TRAP translocon.
Components
  • (Large ribosomal subunit protein ...) x 4
  • (Ribosomal protein ...) x 3
  • (Translocon-associated protein subunit ...) x 4
  • 60S ribosomal protein L39
  • Protein transport protein Sec61 subunit gammaProtein targeting
  • RL22 protein (Fragment)
  • RL26 protein (Fragment)
  • RNA (156-MER)
  • RNA (1766)
  • Sec61a
  • Sec61b
KeywordsTRANSPORT PROTEIN / Membrane protein / protein translocation / protein biogenesis.
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
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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)
MethodELECTRON MICROSCOPY / single 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, 2items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
5: RNA (1766)
8: RNA (156-MER)
A: Translocon-associated protein subunit alpha
B: Translocon-associated protein subunit beta
D: Translocon-associated protein subunit delta
G: Translocon-associated protein subunit gamma
P: Large ribosomal subunit protein uL22
R: Ribosomal protein L19
U: RL22 protein (Fragment)
X: Ribosomal protein L23/L25 N-terminal domain-containing protein
Y: RL26 protein (Fragment)
C: Sec61a
b: Sec61b
d: Large ribosomal subunit protein eL31
g: Protein transport protein Sec61 subunit gamma
h: Large ribosomal subunit protein uL29
j: Ribosomal protein L37
k: Large ribosomal subunit protein eL38
l: 60S ribosomal protein L39


Theoretical massNumber of molelcules
Total (without water)1,548,68719
Polymers1,548,68719
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, PMID: 18611385
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules 58

#1: RNA chain RNA (1766)


Mass: 1186579.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#2: RNA chain RNA (156-MER)


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)

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Translocon-associated protein subunit ... , 4 types, 4 molecules ABDG

#3: Protein Translocon-associated protein subunit alpha


Mass: 39381.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#4: Protein Translocon-associated protein subunit beta


Mass: 20478.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P572
#5: Protein Translocon-associated protein subunit delta


Mass: 18901.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P940
#6: Protein Translocon-associated protein subunit gamma


Mass: 21100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NYA9

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Large ribosomal subunit protein ... , 4 types, 4 molecules Pdhk

#7: Protein Large ribosomal subunit protein uL22


Mass: 21414.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q9T9
#14: Protein Large ribosomal subunit protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PUU0
#16: Protein Large ribosomal subunit protein uL29


Mass: 14591.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3TAC5
#18: Protein Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)

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Ribosomal protein ... , 3 types, 3 molecules RXj

#8: Protein Ribosomal protein L19 /


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PLN0
#10: Protein Ribosomal protein L23/L25 N-terminal domain-containing protein / Ribosome


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3CX48
#17: Protein Ribosomal protein L37 /


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P472

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Protein , 5 types, 5 molecules UYCgl

#9: Protein RL22 protein (Fragment)


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7EJM7
#11: Protein RL26 protein (Fragment)


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A7K9BN74
#12: Protein Sec61a


Mass: 52034.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#15: Protein Protein transport protein Sec61 subunit gamma / Protein targeting


Mass: 9352.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A836CVU8
#19: Protein 60S ribosomal protein L39 /


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)

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Protein/peptide , 1 types, 1 molecules b

#13: Protein/peptide Sec61b


Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mammlian Ribosome Sec61 TRAP complex / Type: RIBOSOME / Details: Mammlian ribosome-Sec61 TRAP complex / Entity ID: #3-#6, #1-#2, #7-#11, #13-#19 / Source: NATURAL
Molecular weightValue: 3.2 MDa / Experimental value: NO
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHepesHepes1
2300 mMPotassium acetateKoAc1
310 mMMagnesium acetateMgAc1
41 mMDithiothritolDDT1
50.003 percentLauryl maltose neopentyl glycolLMNG1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified Ribosome Sec61/TRAP complex
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 30294

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1098031
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61177 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE

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