[English] 日本語
Yorodumi
- PDB-3jc2: The structure of the mammalian Sec61 channel opened by a signal s... -

+
Open data


ID or keywords:

Loading...

-
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


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 / regulation of meiotic cell cycle process involved in oocyte maturation / pronephric nephron development / response to L-arginine ...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 / regulation of meiotic cell cycle process involved in oocyte maturation / pronephric nephron development / response to L-arginine / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / mammary gland development / positive regulation of fatty acid biosynthetic process / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / blastocyst formation / post-translational protein targeting to membrane, translocation / response to food / biosynthetic process / positive regulation of endocytosis / protein transmembrane transporter activity / response to mechanical stimulus / positive regulation of phagocytosis / lactation / response to nutrient levels / female pregnancy / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / phospholipid binding / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of nitric oxide biosynthetic process / ribosome binding / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / inflammatory response / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / 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 (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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3245
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3245
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-3245
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 (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)

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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-ID
13J7Q

3j7q

1
21RH5

1rh5

1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 0 0 3911

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more