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- EMDB-18677: Structure of the PBD of human SRP68/72 (cryoSPARC 3DFlex) -

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Basic information

Entry
Database: EMDB / ID: EMD-18677
TitleStructure of the PBD of human SRP68/72 (cryoSPARC 3DFlex)
Map dataFull map
Sample
  • Complex: SRP68/72
    • Protein or peptide: Signal recognition particle subunit SRP68
    • Protein or peptide: Signal recognition particle subunit SRP72
KeywordsSignal recognition particle / TPR / protein translocation / TRANSLATION
Function / homology
Function and homology information


endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / 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 / protein domain specific binding ...endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / 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 / protein domain specific binding / response to xenobiotic stimulus / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / cytosol
Similarity search - Function
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 / Tetratricopeptide repeat ...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 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhong Y / Feng J / Koh AF / Kotecha A / Greber BJ / Ataide SF
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: 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
DepositionOct 18, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18677.png

Downloads & links

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Map

FileDownload / File: emd_18677.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 180 pix.
= 205.2 Å		1.14 Å/pix.
x 180 pix.
= 205.2 Å		1.14 Å/pix.
x 180 pix.
= 205.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0125
Minimum - Maximum-0.04399466 - 0.08381038
Average (Standard dev.)0.0000683368 (±0.0015233991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 205.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18677_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map from cryoSPARC's 3DFlex

Fileemd_18677_half_map_1.map
AnnotationHalf map from cryoSPARC's 3DFlex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map from cryoSPARC's 3DFlex

Fileemd_18677_half_map_2.map
AnnotationHalf map from cryoSPARC's 3DFlex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : SRP68/72

EntireName: SRP68/72
Components
  • Complex: SRP68/72
    • Protein or peptide: Signal recognition particle subunit SRP68
    • Protein or peptide: Signal recognition particle subunit SRP72

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Supramolecule #1: SRP68/72

SupramoleculeName: SRP68/72 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Signal recognition particle subunit SRP68

MacromoleculeName: Signal recognition particle subunit SRP68 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.617305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Signal recognition particle subunit SRP72

MacromoleculeName: Signal recognition particle subunit SRP72 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.992531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMKClPotassium Chloride
400.0 mMNaClSodium Chloride
10.0 mMMgCl2Magnesium Chloride
50.0 mMHEPES-KOH
0.5 mMTCEP
GridModel: 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. / Details: PIE Scientific Tergeo plasma cleaner
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsCollected movies in EER format.
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Initial reference generated from refining of a particle subset against a rod-like density.
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: 3D flexible refinement in cryoSPARC / Number images used: 145826
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: 3D flexible refinement in cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 4)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qvx:
Structure of the PBD of human SRP68/72 (cryoSPARC 3DFlex)

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