+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12304 | |||||||||
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Title | SRP54 and SRP RNA proximal site | |||||||||
Map data | focused refinement of state A | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | Jomaa A / Ban N | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER. Authors: Jae Ho Lee / Ahmad Jomaa / SangYoon Chung / Yu-Hsien Hwang Fu / Ruilin Qian / Xuemeng Sun / Hao-Hsuan Hsieh / Sowmya Chandrasekar / Xiaotian Bi / Simone Mattei / Daniel Boehringer / Shimon ...Authors: Jae Ho Lee / Ahmad Jomaa / SangYoon Chung / Yu-Hsien Hwang Fu / Ruilin Qian / Xuemeng Sun / Hao-Hsuan Hsieh / Sowmya Chandrasekar / Xiaotian Bi / Simone Mattei / Daniel Boehringer / Shimon Weiss / Nenad Ban / Shu-Ou Shan / Abstract: The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP ...The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)-driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54 linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12304.map.gz | 314.6 MB | EMDB map data format | |
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Header (meta data) | emd-12304-v30.xml emd-12304.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_12304.png | 20.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12304 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12304 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12304.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | focused refinement of state A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.062 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ribosome nascent chain complex with SRP and SRP receptor
Entire | Name: ribosome nascent chain complex with SRP and SRP receptor |
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Components |
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-Supramolecule #1: ribosome nascent chain complex with SRP and SRP receptor
Supramolecule | Name: ribosome nascent chain complex with SRP and SRP receptor type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 3.5 MDa |
-Macromolecule #1: SRP RNA and SRP54
Macromolecule | Name: SRP RNA and SRP54 / type: rna / ID: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: LADLGRKITS ALRSLSNATI INEEVLNAML KEVCTALLEA DVNIKLVKQL RENVKSAIDL EEMASGLNK RKMIQHAVFK ELVKLVDPGV KAWTPTKGKQ NVIMFVGLQG SGKTTTCSKL AYYYQRKGWK TCLICADTFR AGAFDQLKQ NATKARIPFY GSYTEMDPVI ...String: LADLGRKITS ALRSLSNATI INEEVLNAML KEVCTALLEA DVNIKLVKQL RENVKSAIDL EEMASGLNK RKMIQHAVFK ELVKLVDPGV KAWTPTKGKQ NVIMFVGLQG SGKTTTCSKL AYYYQRKGWK TCLICADTFR AGAFDQLKQ NATKARIPFY GSYTEMDPVI IASEGVEKFK NENFEIIIVD TSGRHKQEDS LFEEMLQVAN A IQPDNIVY VMDASIEQAC EAQAKAFKDK VDVASVIVTK LDGHAKGGGA LSAVAATKSP IIFIGTGEHI DD FEPFKTQ PFISKLLGMG DIEGLIDKVN ELKLDDNEAL IEKLKHGQFT LRDMYEQFQN IMKMGPGNEQ ESM ARLKKL MTIMDSMNDQ ELDSTDGAKV FSKQPGRIQR VARGSGVSTR DVQELLTQYT KFAQMVKKMG GI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
Details | in-vitro translation system |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Startup model | Type of model: INSILICO MODEL / In silico model: using SGD from particles |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33821 |