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- PDB-3jc2: The structure of the mammalian Sec61 channel opened by a signal s... -

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Basic information

Entry
Database: PDB / ID: 3jc2
TitleThe structure of the mammalian Sec61 channel opened by a signal sequence
Components
  • Prolactin
  • Protein transport protein Sec61 subunit alpha isoform 1
  • Protein transport protein Sec61 subunit beta
  • Protein transport protein Sec61 subunit gamma
KeywordsTRANSPORT PROTEIN / Sec61 / translocation / signal sequence
Function / homology
Function and homology information


positive regulation of biosynthetic process / long-day photoperiodism / response to external biotic stimulus / prolactin receptor binding / peptide hormone secretion / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of lactation / pronephric nephron development / response to L-arginine ...positive regulation of biosynthetic process / long-day photoperiodism / response to external biotic stimulus / prolactin receptor binding / peptide hormone secretion / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of lactation / pronephric nephron development / response to L-arginine / regulation of meiotic cell cycle process involved in oocyte maturation / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / positive regulation of fatty acid biosynthetic process / signal sequence binding / mammary gland development / post-translational protein targeting to membrane, translocation / blastocyst formation / biosynthetic process / response to food / positive regulation of endocytosis / protein transmembrane transporter activity / response to mechanical stimulus / lactation / positive regulation of phagocytosis / positive regulation of receptor signaling pathway via JAK-STAT / response to nutrient levels / female pregnancy / positive regulation of non-canonical NF-kappaB signal transduction / hormone activity / phospholipid binding / positive regulation of nitric oxide biosynthetic process / ribosome binding / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / endoplasmic reticulum lumen / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / extracellular space / extracellular region / metal ion binding / cytosol
Similarity search - Function
Preprotein translocase SecE subunit / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p ...Preprotein translocase SecE subunit / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / 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 / Four-helical cytokine-like, core / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Prolactin / Protein transport protein Sec61 subunit alpha isoform 1 / Protein transport protein Sec61 subunit gamma / Prolactin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Canis lupus familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsVoorhees, R.M. / Hegde, R.S.
CitationJournal: Science / Year: 2016
Title: Structure of the Sec61 channel opened by a signal sequence.
Authors: Rebecca M Voorhees / Ramanujan S Hegde /
Abstract: Secreted and integral membrane proteins compose up to one-third of the biological proteome. These proteins contain hydrophobic signals that direct their translocation across or insertion into the ...Secreted and integral membrane proteins compose up to one-third of the biological proteome. These proteins contain hydrophobic signals that direct their translocation across or insertion into the lipid bilayer by the Sec61 protein-conducting channel. The molecular basis of how hydrophobic signals within a nascent polypeptide trigger channel opening is not understood. Here, we used cryo-electron microscopy to determine the structure of an active Sec61 channel that has been opened by a signal sequence. The signal supplants helix 2 of Sec61α, which triggers a rotation that opens the central pore both axially across the membrane and laterally toward the lipid bilayer. Comparisons with structures of Sec61 in other states suggest a pathway for how hydrophobic signals engage the channel to gain access to the lipid bilayer.
History
DepositionNov 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
1: Protein transport protein Sec61 subunit alpha isoform 1
2: Protein transport protein Sec61 subunit gamma
w: Prolactin
3: Protein transport protein Sec61 subunit beta


Theoretical massNumber of molelcules
Total (without water)64,0944
Polymers64,0944
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein transport protein Sec61 subunit alpha isoform 1 / Sec61 alpha-1


Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from native canine microsomes / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P38377
#2: Protein Protein transport protein Sec61 subunit gamma


Mass: 7019.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from native canine microsomes / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P60058
#3: Protein/peptide Prolactin


Mass: 2053.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: prolactin / Production host: Oryctolagus cuniculus (rabbit)
Tissue fraction (production host): reticulocyte translation extract in the presence of canine microsomes
References: UniProt: Q6VMP1, UniProt: P01239*PLUS
#4: Protein/peptide Protein transport protein Sec61 subunit beta / Sec61 beta


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from native canine microsomes / Source: (natural) Canis lupus familiaris (dog)
Has protein modificationN

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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

Component
IDNameTypeParent-ID
1Sec61 protein conducting channel opened by the pre-prolactin signal sequenceCOMPLEX0
2Sec61 alpha1
3Sec61 gamma1
4Sec61 beta1
5Pre-prolactin nascent chain1
Buffer solutionName: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
pH: 7.5
Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil (R2/2) holey carbon grid covered in a 70 Angstrom-thick layer of amorphous carbon
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %
Details: 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds, and then plunged into liquid ethane (FEI VITROBOT).
Method: 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 6, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2REFMACmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Num. of particles: 101339 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingSpace: REAL / Target criteria: R-factor
Details: DETAILS--Real-space fitting using Chimera and Coot followed by reciprocal-space refinement using REFMAC
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13J7Q

3j7q

13J7Q1PDBexperimental model
21RH5

1rh5

11RH52PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 0 0 3911

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