[English] 日本語
Yorodumi
- PDB-7obq: SRP-SR at the distal site conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7obq
TitleSRP-SR at the distal site conformation
Components
  • (Signal recognition particle ...) x 5
  • EM14S01-3B_G0054400.mRNA.1.CDS.1
  • SRP RNA
  • SRP receptor subunit alpha
KeywordsRNA BINDING PROTEIN / SRP SRP receptor / co-translational protein targeting / endoplasmic reticulum / signal peptide
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / protein targeting to ER / granulocyte differentiation / signal-recognition-particle GTPase / protein localization to Golgi apparatus ...SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / protein targeting to ER / granulocyte differentiation / signal-recognition-particle GTPase / protein localization to Golgi apparatus / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / Golgi to plasma membrane protein transport / SRP-dependent cotranslational protein targeting to membrane / exocrine pancreas development / TPR domain binding / membrane => GO:0016020 / aminopeptidase activity / ribonucleoprotein complex binding / cytoplasmic microtubule / neutrophil chemotaxis / intracellular protein transport / GDP binding / ribosome binding / nuclear speck / serine-type endopeptidase activity / GTPase activity / endoplasmic reticulum membrane / GTP binding / nucleolus / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / nucleus / cytosol
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / 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 receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / 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 / Beta-Lactamase - #60 / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Longin-like domain superfamily / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Tetratricopeptide repeat / Beta-Lactamase / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Alpha/Beta hydrolase fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / SRP receptor subunit alpha / EM14S01-3B_G0054400.mRNA.1.CDS.1 / Signal recognition particle receptor subunit beta / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP72 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / SRP receptor subunit alpha / EM14S01-3B_G0054400.mRNA.1.CDS.1 / Signal recognition particle receptor subunit beta / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP54 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Oryctolagus cuniculus (rabbit)
Canis lupus familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJomaa, A. / Ban, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Cell Rep / Year: 2021
Title: Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle.
Authors: Ahmad Jomaa / Simon Eitzinger / Zikun Zhu / Sowmya Chandrasekar / Kan Kobayashi / Shu-Ou Shan / Nenad Ban /
Abstract: Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many ...Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles. Due to its complexity, the mammalian SRP targeting process is mechanistically not well understood. In particular, it is not clear how SRP recognizes translating ribosomes with exposed signal sequences and how the GTPase activity of SRP and SR is regulated. Here, we present electron cryo-microscopy structures of SRP and SRP·SR in complex with the translating ribosome. The structures reveal the specific molecular interactions between SRP and the emerging signal sequence and the elements that regulate GTPase activity of SRP·SR. Our results suggest the molecular mechanism of how eukaryote-specific elements regulate the early and late stages of SRP-dependent protein targeting.
#1: Journal: Cell Rep / Year: 2021
Title: Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle
Authors: Jomaa, A. / Eitzinger, S. / Zhu, Z. / Chandrasekar, S. / Kobayashi, K. / Shan, S. / Ban, N.
History
DepositionApr 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jul 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / 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 / _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-12799
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12799
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: SRP RNA
q: Signal recognition particle 19
s: EM14S01-3B_G0054400.mRNA.1.CDS.1
u: Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68
v: Signal recognition particle receptor subunit beta
x: Signal recognition particle 54 kDa protein
y: SRP receptor subunit alpha
z: Signal recognition particle subunit SRP72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,87914
Polymers399,2398
Non-polymers1,6406
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24560 Å2
ΔGint-156 kcal/mol
Surface area103790 Å2

-
Components

-
RNA chain , 1 types, 1 molecules 1

#1: RNA chain SRP RNA


Mass: 80701.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)

-
Signal recognition particle ... , 5 types, 5 molecules quvxz

#2: Protein Signal recognition particle 19


Mass: 16183.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: J9PAS6
#4: Protein Signal recognition particle subunit SRP68,Signal recognition particle subunit SRP68 / SRP68 / Signal recognition particle 68 kDa protein


Mass: 67082.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q00004
#5: Protein Signal recognition particle receptor subunit beta


Mass: 29846.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SRPRB / Production host: Escherichia coli (E. coli) / References: UniProt: G1STG2
#6: Protein Signal recognition particle 54 kDa protein / SRP54


Mass: 55775.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P61010
#8: Protein Signal recognition particle subunit SRP72 / SRP72 / Signal recognition particle 72 kDa protein


Mass: 74608.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P33731

-
Protein , 2 types, 2 molecules sy

#3: Protein EM14S01-3B_G0054400.mRNA.1.CDS.1


Mass: 5294.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS2833 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7I9EWR8
#7: Protein SRP receptor subunit alpha


Mass: 69745.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: SRPRA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5F9CI80

-
Non-polymers , 3 types, 6 molecules

#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#11: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SRP-SR complexCOMPLEX#1-#80MULTIPLE SOURCES
2SRP-SR complexCOMPLEX#1-#2, #4, #6, #81NATURAL
3EM14S01-3B_G0054400.mRNA.1.CDS.1COMPLEX#31RECOMBINANT
4Signal recognition particle receptor subunitCOMPLEX#5, #71RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Canis lupus familiaris (dog)9615
23Saccharomyces cerevisiae (brewer's yeast)4932
34Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Oryctolagus cuniculus (rabbit)9986
24Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE-PROPANE

-
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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155989 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6FRK

6frk


Accession code: 6FRK / Source name: PDB / Type: experimental model

+
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