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- PDB-1ry1: Structure of the signal recognition particle interacting with the... -

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Basic information

Entry
Database: PDB / ID: 1ry1
TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome
Components
  • (SRP RNASignal recognition particle RNA) x 6
  • SRP Alu domain
  • SRP S domain
  • SRP14
  • SRP19
  • SRP54M
  • SRP54NG
  • SRP9Signal recognition particle 9
  • signal sequence peptide
KeywordsTRANSLATION / signal recognition particle / RNA binding
Function / homology
Function and homology information


signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / absorption of visible light / negative regulation of translational elongation / G protein-coupled photoreceptor activity ...signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / absorption of visible light / negative regulation of translational elongation / G protein-coupled photoreceptor activity / signal recognition particle / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / cotranslational protein targeting to membrane / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / photoreceptor outer segment membrane / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / visual perception / neutrophil chemotaxis / photoreceptor disc membrane / GDP binding / secretory granule lumen / ficolin-1-rich granule lumen / nuclear body / nuclear speck / GTPase activity / Neutrophil degranulation / GTP binding / nucleolus / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular region / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily ...Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Signal recognition particle protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Signal recognition particle protein / Rhodopsin / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP54 / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Triticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsHalic, M. / Becker, T. / Pool, M.R. / Spahn, C.M. / Grassucci, R.A. / Frank, J. / Beckmann, R.
CitationJournal: Nature / Year: 2004
Title: Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
Authors: Mario Halic / Thomas Becker / Martin R Pool / Christian M T Spahn / Robert A Grassucci / Joachim Frank / Roland Beckmann /
Abstract: Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal ...Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal recognition particle (SRP), an evolutionarily conserved ribonucleoprotein particle. SRP recognizes signal sequences of nascent protein chains emerging from the ribosome. Subsequent binding of SRP leads to a pause in peptide elongation and to the ribosome docking to the membrane-bound SRP receptor. Here we present the structure of a targeting complex consisting of mammalian SRP bound to an active 80S ribosome carrying a signal sequence. This structure, solved to 12 A by cryo-electron microscopy, enables us to generate a molecular model of SRP in its functional conformation. The model shows how the S domain of SRP contacts the large ribosomal subunit at the nascent chain exit site to bind the signal sequence, and that the Alu domain reaches into the elongation-factor-binding site of the ribosome, explaining its elongation arrest activity.
History
DepositionDec 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: em_entity_assembly / em_entity_assembly_naturalsource ...em_entity_assembly / em_entity_assembly_naturalsource / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_entity_src_syn / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Assembly

Deposited unit
E: SRP Alu domain
A: SRP S domain
M: SRP RNA
N: SRP RNA
O: SRP RNA
P: SRP RNA
Q: SRP RNA
R: SRP RNA
C: SRP9
D: SRP14
B: SRP19
U: SRP54NG
W: SRP54M
S: signal sequence peptide


Theoretical massNumber of molelcules
Total (without water)179,84614
Polymers179,84614
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 8 types, 8 molecules EAMNOPQR

#1: RNA chain SRP Alu domain


Mass: 16277.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#2: RNA chain SRP S domain


Mass: 41566.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#3: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 8784.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#4: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 9807.837 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#5: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 7695.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#6: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 6325.847 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#7: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 3844.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#8: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 3804.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)

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Protein , 5 types, 5 molecules CDBUW

#9: Protein SRP9 / Signal recognition particle 9


Mass: 9996.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / Genus: Homo / References: UniProt: P49458*PLUS
#10: Protein SRP14


Mass: 12114.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / Genus: Homo / References: UniProt: P37108
#11: Protein SRP19


Mass: 12561.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / Genus: Homo / References: UniProt: P09132*PLUS
#12: Protein SRP54NG


Mass: 32472.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / Genus: Thermus / References: UniProt: O07347*PLUS
#13: Protein SRP54M


Mass: 12473.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / Genus: Mus / References: UniProt: P14576*PLUS

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Protein/peptide , 1 types, 1 molecules S

#14: Protein/peptide signal sequence peptide


Mass: 2121.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Triticum aestivum (bread wheat) / References: UniProt: O62798*PLUS

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Details

Sequence detailsThis structure has been modeled using polymer sequences from other organisms, including Homo ...This structure has been modeled using polymer sequences from other organisms, including Homo sapiens (chains C,D,E), Thermus aquaticus (chain U), Mus musculus (chain W), and Tursiops truncatus (chain S).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1signal recognition particle interacting with elongation-arrested ribosomeCOMPLEXall0MULTIPLE SOURCES
2signal recognition particleCOMPLEX#1-#131NATURAL
380S ribosome nascent chain complexRIBOSOME#141NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Canis lupus familiaris (dog)9615
23Triticum aestivum (bread wheat)4565
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: PLUNGED INTO ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2000
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 51000 X / Calibrated magnification: 52000 X / Nominal defocus max: 45000 nm / Nominal defocus min: 10000 nm / Cs: 2 mm
Specimen holderTemperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 75

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Processing

EM software
IDNameCategory
1SPIDER3D reconstruction
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.5 CUT-OFF
Details: The chains M, N, O, P, Q and R are fragments of a double helical strand of RNA. The author maintains that some of the residues could not be modeled correctly due to limited resolution in this region.
Symmetry type: POINT
RefinementHighest resolution: 12 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5335 6459 0 0 11794

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