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Open data
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Basic information
Entry | Database: PDB / ID: 7obq | ||||||
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Title | SRP-SR at the distal site conformation | ||||||
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![]() | RNA BINDING PROTEIN / SRP SRP receptor / co-translational protein targeting / endoplasmic reticulum / signal peptide | ||||||
Function / homology | ![]() SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal-recognition-particle GTPase / protein targeting to ER / 7S RNA binding ...SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal-recognition-particle GTPase / protein targeting to ER / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / cytoplasmic microtubule / aminopeptidase activity / vesicle-mediated transport / neutrophil chemotaxis / intracellular protein transport / GDP binding / membrane => GO:0016020 / nuclear speck / serine-type endopeptidase activity / GTPase activity / endoplasmic reticulum membrane / nucleolus / GTP binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Jomaa, A. / Ban, N. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 414.7 KB | Display | ![]() |
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PDB format | ![]() | 310 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12799MC ![]() 7obrC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 1 types, 1 molecules 1
#1: RNA chain | Mass: 80701.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Signal recognition particle ... , 5 types, 5 molecules quvxz
#2: Protein | Mass: 16183.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein | Mass: 67082.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 29846.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#6: Protein | Mass: 55775.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 74608.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules sy
#3: Protein | Mass: 5294.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS2833 / Production host: ![]() ![]() |
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#7: Protein | Mass: 69745.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 3 types, 6 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/GNP.gif)
#9: Chemical | #10: Chemical | ChemComp-GTP / | #11: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155989 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | PDB-ID: 6FRK Accession code: 6FRK / Source name: PDB / Type: experimental model |