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- PDB-4p3e: Structure of the human SRP S domain -

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Basic information

Entry
Database: PDB / ID: 4p3e
TitleStructure of the human SRP S domain
Components
  • SRP RNA (124-mer)
  • Signal recognition particle 19 kDa protein
  • Signal recognition particle subunit SRP68
KeywordsRNA BINDING PROTEIN/RNA / SRP / SRP RNA / SRP19 / SRP68 / ribonucleoprotein particle (RNP) / Arginine-rich motif (ARM) / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


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 / signal recognition particle / cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / nuclear body ...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 / signal recognition particle / cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / nuclear body / ribosome / protein domain specific binding / response to xenobiotic stimulus / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / cytosol
Similarity search - Function
Signal recognition particle, SRP68 subunit, RNA-binding domain / Hyaluronidase domain-like / Signal recognition particle, SRP19-like subunit / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein ...Signal recognition particle, SRP68 subunit, RNA-binding domain / Hyaluronidase domain-like / Signal recognition particle, SRP19-like subunit / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGrotwinkel, J.T. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB638 Germany
CitationJournal: Science / Year: 2014
Title: SRP RNA remodeling by SRP68 explains its role in protein translocation.
Authors: Grotwinkel, J.T. / Wild, K. / Segnitz, B. / Sinning, I.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Data collection
Revision 1.2Jul 9, 2014Group: Structure summary
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SRP RNA (124-mer)
B: Signal recognition particle 19 kDa protein
C: Signal recognition particle subunit SRP68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0427
Polymers80,9443
Non-polymers974
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-62 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.649, 70.530, 106.493
Angle α, β, γ (deg.)90.000, 100.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain SRP RNA (124-mer)


Mass: 40549.184 Da / Num. of mol.: 1 / Fragment: GB residues 234-358 / Mutation: C114G, G237U, G238A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 177793
#2: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 14791.062 Da / Num. of mol.: 1 / Fragment: UNP residues 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP19 / Production host: Escherichia coli (E. coli) / References: UniProt: P09132
#3: Protein Signal recognition particle subunit SRP68 / SRP68 / Signal recognition particle 68 kDa protein


Mass: 25604.229 Da / Num. of mol.: 1 / Fragment: UNP residues 47-254 / Mutation: E108D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB9
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: Ammonium sulfate, Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.5→44.09 Å / Num. obs: 11703 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 92.36 Å2 / Net I/σ(I): 9
Reflection shellResolution: 3.5→3.85 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.36 / Rsym value: 0.021 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3F and 3KTV

4p3f

3ktv


Resolution: 3.5→44.089 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 550 4.74 %
Rwork0.2437 11052 -
obs0.2456 11602 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.42 Å2 / Biso mean: 55.7406 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3.5→44.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 2666 4 0 5011
Biso mean--13.43 --
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055511
X-RAY DIFFRACTIONf_angle_d1.0248085
X-RAY DIFFRACTIONf_chiral_restr0.059995
X-RAY DIFFRACTIONf_plane_restr0.004542
X-RAY DIFFRACTIONf_dihedral_angle_d18.1432490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5001-3.85220.39891280.33492702283097
3.8522-4.40910.34581350.2712750288599
4.4091-5.55330.31951500.24742761291199
5.5533-44.0920.21831370.206928392976100

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