+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18674 | |||||||||
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Title | Structure of nPBD of human SRP68/72 | |||||||||
Map data | Postprocessed EM map | |||||||||
Sample |
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Keywords | Signal recognition particle / TPR / protein translocation / TRANSLATION | |||||||||
Function / homology | Function and homology information signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome / response to xenobiotic stimulus ...signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome / response to xenobiotic stimulus / protein domain specific binding / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Zhong Y / Feng J / Koh AF / Kotecha A / Greber BJ / Ataide SF | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2024 Title: Cryo-EM structure of SRP68/72 reveals an extended dimerization domain with RNA-binding activity. Authors: Yichen Zhong / Junjie Feng / Adrian F Koh / Abhay Kotecha / Basil J Greber / Sandro F Ataide / Abstract: The signal recognition particle (SRP) is a critical component in protein sorting pathways in all domains of life. Human SRP contains six proteins bound to the 7S RNA and their structures and ...The signal recognition particle (SRP) is a critical component in protein sorting pathways in all domains of life. Human SRP contains six proteins bound to the 7S RNA and their structures and functions have been mostly elucidated. The SRP68/72 dimer is the largest SRP component and is essential for SRP function. Although the structures of the SRP68/72 RNA binding and dimerization domains have been previously reported, the structure and function of large portions of the SRP68/72 dimer remain unknown. Here, we analyse full-length SRP68/72 using cryo-EM and report that SRP68/72 depend on each other for stability and form an extended dimerization domain. This newly observed dimerization domain is both a protein- and RNA-binding domain. Comparative analysis with current structural models suggests that this dimerization domain undergoes dramatic translocation upon SRP docking onto SRP receptor and eventually comes close to the Alu domain. We propose that the SRP68/72 dimerization domain functions by binding and detaching the Alu domain and SRP9/14 from the ribosomal surface, thus releasing elongation arrest upon docking onto the ER membrane. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18674.map.gz | 20.9 MB | EMDB map data format | |
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Header (meta data) | emd-18674-v30.xml emd-18674.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
Images | emd_18674.png | 68 KB | ||
Masks | emd_18674_msk_1.map | 22.2 MB | Mask map | |
Filedesc metadata | emd-18674.cif.gz | 6.9 KB | ||
Others | emd_18674_half_map_1.map.gz emd_18674_half_map_2.map.gz | 17 MB 17 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18674 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18674 | HTTPS FTP |
-Validation report
Summary document | emd_18674_validation.pdf.gz | 848.2 KB | Display | EMDB validaton report |
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Full document | emd_18674_full_validation.pdf.gz | 847.7 KB | Display | |
Data in XML | emd_18674_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | emd_18674_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18674 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18674 | HTTPS FTP |
-Related structure data
Related structure data | 8qvwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18674.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Postprocessed EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18674_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map
File | emd_18674_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map
File | emd_18674_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SRP68/72
Entire | Name: SRP68/72 |
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Components |
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-Supramolecule #1: SRP68/72
Supramolecule | Name: SRP68/72 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 140 KDa |
-Macromolecule #1: Signal recognition particle subunit SRP68
Macromolecule | Name: Signal recognition particle subunit SRP68 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 66.617305 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKEFGDSLSL EILQIIKESQ QQHGLRHGDF QRYRGYCSRR QRRLRKTLNF KMGNRHKFTG KKVTEELLTD NRYLLLVLMD AERAWSYAM QLKQEANTEP RKRFHLLSRL RKAVKHAEEL ERLCESNRVD AKTKLEAQAY TAYLSGMLRF EHQEWKAAIE A FNKCKTIY ...String: MKEFGDSLSL EILQIIKESQ QQHGLRHGDF QRYRGYCSRR QRRLRKTLNF KMGNRHKFTG KKVTEELLTD NRYLLLVLMD AERAWSYAM QLKQEANTEP RKRFHLLSRL RKAVKHAEEL ERLCESNRVD AKTKLEAQAY TAYLSGMLRF EHQEWKAAIE A FNKCKTIY EKLASAFTEE QAVLYNQRVE EISPNIRYCA YNIGDQSAIN ELMQMRLRSG GTEGLLAEKL EALITQTRAK QA ATMSEVE WRGRTVPVKI DKVRIFLLGL ADNEAAIVQA ESEETKERLF ESMLSECRDA IQVVREELKP DQKQRDYILE GEP GKVSNL QYLHSYLTYI KLSTAIKRNE NMAKGLQRAL LQQQPEDDSK RSPRPQDLIR LYDIILQNLV ELLQLPGLEE DKAF QKEIG LKTLVFKAYR CFFIAQSYVL VKKWSEALVL YDRVLKYANE VNSDAGAFKN SLKDLPDVQE LITQVRSEKC SLQAA AILD ANDAHQTETS SSQVKDNKPL VERFETFCLD PSLVTKQANL VHFPPGFQPI PCKPLFFDLA LNHVAFPPLE DKLEQK TKS GLTGYIKGIF GFRS UniProtKB: Signal recognition particle subunit SRP68 |
-Macromolecule #2: Signal recognition particle subunit SRP72
Macromolecule | Name: Signal recognition particle subunit SRP72 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 74.992531 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SNAMASGGSG GVSVPALWSE VNRYGQNGDF TRALKTVNKI LQINKDDVTA LHCKVVCLIQ NGSFKEALNV INTHTKVLAN NSLSFEKAY CEYRLNRIEN ALKTIESANQ QTDKLKELYG QVLYRLERYD ECLAVYRDLV RNSQDDYDEE RKTNLSAVVA A QSNWEKVV ...String: SNAMASGGSG GVSVPALWSE VNRYGQNGDF TRALKTVNKI LQINKDDVTA LHCKVVCLIQ NGSFKEALNV INTHTKVLAN NSLSFEKAY CEYRLNRIEN ALKTIESANQ QTDKLKELYG QVLYRLERYD ECLAVYRDLV RNSQDDYDEE RKTNLSAVVA A QSNWEKVV PENLGLQEGT HELCYNTACA LIGQGQLNQA MKILQKAEDL CRRSLSEDTD GTEEDPQAEL AIIHGQMAYI LQ LQGRTEE ALQLYNQIIK LKPTDVGLLA VIANNIITIN KDQNVFDSKK KVKLTNAEGV EFKLSKKQLQ AIEFNKALLA MYT NQAEQC RKISASLQSQ SPEHLLPVLI QAAQLCREKQ HTKAIELLQE FSDQHPENAA EIKLTMAQLK ISQGNISKAC LILR SIEEL KHKPGMVSAL VTMYSHEEDI DSAIEVFTQA IQWYQNHQPK SPAHLSLIRE AANFKLKYGR KKEAISDLQQ LWKQN PKDI HTLAQLISAY SLVDPEKAKA LSKHLPSSDS MSLKVDVEAL ENSAGATYIR KKGGKVTGDS QPKEQGQGDL KKKKKK KKG KLPKNYDPKV TPDPERWLPM RERSYYRGRK KGKKKDQIGK GTQGATAGAS SELDASKTVS SPPTSPRPGS AATVSAS TS NIIPPRHQKP AGAPATKKKQ QQKKKKGGKG GW UniProtKB: Signal recognition particle subunit SRP72 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 18601 / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 245614 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-8qvw: |