- EMDB-16017: Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-16017
Title
Molecular 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
Keywords
Membrane 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 L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / 60S ribosomal protein L19 / 60S ribosomal protein L35 / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L31e, conserved site / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L31e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal protein L37ae/L37e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / 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 L22 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Zinc-binding ribosomal protein / KOW motif / KOW / 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 species
Ovis aries (sheep)
Method
single particle reconstruction / cryo EM / Resolution: 2.69 Å
Journal: 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.
Name: 60S ribosomal protein L39 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)
Organism: Ovis aries (sheep)
Molecular weight
Theoretical: 6.426759 KDa
Sequence
String:
MSSHKTFRIK RFLAKKQKQN RPIPQWIRMK TGNKIRYNSK RRHWRRTKLG L
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.1 mg/mL
Buffer
pH: 7.4 Component:
Concentration
Formula
Name
50.0 mM
Hepes
Hepes
300.0 mM
KoAc
Potassium acetate
10.0 mM
MgAc
Magnesium acetate
1.0 mM
DDT
Dithiothritol
0.003 percent
LMNG
Lauryl maltose neopentyl glycol
Grid
Model: 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
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