[English] 日本語
Yorodumi
- PDB-8qvw: Cryo-EM structure of the peptide binding domain of human SRP68/72 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qvw
TitleCryo-EM structure of the peptide binding domain of human SRP68/72
Components
  • Signal recognition particle subunit SRP68
  • Signal recognition particle subunit SRP72
KeywordsTRANSLATION / Signal recognition particle / TPR / protein translocation
Function / homology
Function and homology information


signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / signal recognition particle / endoplasmic reticulum signal peptide binding / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome binding / ribosome ...signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / signal recognition particle / endoplasmic reticulum signal peptide binding / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome binding / ribosome / response to xenobiotic stimulus / protein domain specific binding / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / cytosol
Similarity search - Function
Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Tetratricopeptide repeat ...Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhong, Y. / Feng, J. / Koh, A.F. / Kotecha, A. / Greber, B.J. / Ataide, S.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of nPBD of human SRP68/72
Authors: Zhong, Y. / Feng, J. / Koh, A.F. / Kotecha, A. / Greber, B.J. / Ataide, S.F.
History
DepositionOct 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal recognition particle subunit SRP68
B: Signal recognition particle subunit SRP72


Theoretical massNumber of molelcules
Total (without water)141,6102
Polymers141,6102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Signal recognition particle subunit SRP68


Mass: 66617.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q9UHB9
#2: Protein Signal recognition particle subunit SRP72


Mass: 74992.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP72 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: O76094

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: SRP68/72 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 Rosetta
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMPotassium ChlorideKCl1
2400 mMSodium ChlorideNaCl1
310 mMMagnesium ChlorideMgCl21
450 mMHEPES-KOH1
50.5 mMTCEP1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 245614 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18601
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selectionBlob and template picking
2Topazparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF Chimeramodel fitting
10PHENIXmodel refinement
11RELION3initial Euler assignment
12RELION5final Euler assignment
13RELION5classification
14RELION53D reconstruction
Image processingDetails: Collected movies in EER format.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38514 / Algorithm: FOURIER SPACE / Details: BLUSH regularisation in RELION 5 used. / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033983
ELECTRON MICROSCOPYf_angle_d0.6965383
ELECTRON MICROSCOPYf_dihedral_angle_d4.177520
ELECTRON MICROSCOPYf_chiral_restr0.041620
ELECTRON MICROSCOPYf_plane_restr0.003694

+
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://pdbjlvh1.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