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Yorodumi- PDB-6frk: Structure of a prehandover mammalian ribosomal SRP and SRP recept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6frk | |||||||||
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Title | Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex | |||||||||
Components |
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Keywords | TRANSLATION / ER membrane targeting ribosome Signal recognition particle | |||||||||
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 / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / endoplasmic reticulum signal peptide binding / negative regulation of translational elongation / signal-recognition-particle GTPase / protein targeting to ER ...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 / signal recognition particle binding / endoplasmic reticulum signal peptide binding / negative regulation of translational elongation / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / cytoplasmic microtubule / neutrophil chemotaxis / GDP binding / ribosome binding / nuclear speck / GTPase activity / endoplasmic reticulum membrane / nucleolus / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Oryctolagus cuniculus (rabbit) Canis lupus familiaris (dog) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Kobayashi, K. / Jomaa, A. / Ban, N. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Science / Year: 2018 Title: Structure of a prehandover mammalian ribosomal SRP·SRP receptor targeting complex. Authors: Kan Kobayashi / Ahmad Jomaa / Jae Ho Lee / Sowmya Chandrasekar / Daniel Boehringer / Shu-Ou Shan / Nenad Ban / Abstract: Signal recognition particle (SRP) targets proteins to the endoplasmic reticulum (ER). SRP recognizes the ribosome synthesizing a signal sequence and delivers it to the SRP receptor (SR) on the ER ...Signal recognition particle (SRP) targets proteins to the endoplasmic reticulum (ER). SRP recognizes the ribosome synthesizing a signal sequence and delivers it to the SRP receptor (SR) on the ER membrane followed by the transfer of the signal sequence to the translocon. Here, we present the cryo-electron microscopy structure of the mammalian translating ribosome in complex with SRP and SR in a conformation preceding signal sequence handover. The structure visualizes all eukaryotic-specific SRP and SR proteins and reveals their roles in stabilizing this conformation by forming a large protein assembly at the distal site of SRP RNA. We provide biochemical evidence that the guanosine triphosphate hydrolysis of SRP·SR is delayed at this stage, possibly to provide a time window for signal sequence handover to the translocon. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6frk.cif.gz | 4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6frk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6frk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6frk_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6frk_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6frk_validation.xml.gz | 267.8 KB | Display | |
Data in CIF | 6frk_validation.cif.gz | 458.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/6frk ftp://data.pdbj.org/pub/pdb/validation_reports/fr/6frk | HTTPS FTP |
-Related structure data
Related structure data | 4300MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules 12578
#1: RNA chain | Mass: 96826.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: REF: 577019609 |
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#2: RNA chain | Mass: 24437.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#5: RNA chain | Mass: 1185357.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#7: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#8: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
+Ribosomal protein ... , 41 types, 41 molecules 34ABCDEFGHIJLMNOPQRSTUVWXYacde...
-60S ribosomal protein ... , 2 types, 2 molecules Zb
#33: Protein | Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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#35: Protein | Mass: 8722.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
-Signal recognition particle ... , 6 types, 6 molecules qruwxz
#50: Protein | Mass: 12159.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: J9PAS6 |
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#51: Protein | Mass: 67314.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P33731 |
#53: Protein | Mass: 65569.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q00004 |
#55: Protein | Mass: 8694.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P21262 |
#56: Protein | Mass: 55775.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P61010 |
#58: Protein | Mass: 12512.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P16255 |
-SRP receptor ... , 2 types, 2 molecules vy
#54: Protein | Mass: 23588.018 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 |
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#57: Protein | Mass: 72232.578 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: G1TCX6 |
-Protein / Protein/peptide , 2 types, 2 molecules 6t
#52: Protein/peptide | Mass: 1262.751 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Oryctolagus cuniculus (rabbit) |
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#6: Protein | Mass: 22217.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
-Non-polymers , 4 types, 139 molecules
#59: Chemical | ChemComp-MG / #60: Chemical | #61: Chemical | ChemComp-GTP / | #62: Chemical | |
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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 |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45800 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL |