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- PDB-1l9a: CRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL... -

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Basic information

Entry
Database: PDB / ID: 1l9a
TitleCRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL RECOGNITION PARTICLE RNA
Components
  • SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
  • signal recognition particle RNA S domain
KeywordsSIGNALING PROTEIN/RNA / PROTEIN-RNA COMPLEX / RIBONUCLEOPROTEIN / SRP / SIGNAL RECOGNITION PARTICLE / TETRALOOP / SIGNALING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane
Similarity search - Function
Signal recognition particle, SRP19 subunit, archaeal-type / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYL MERCURY ION / : / RNA / RNA (> 10) / RNA (> 100) / Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsOubridge, C. / Kuglstatter, A. / Jovine, L. / Nagai, K.
CitationJournal: Mol.Cell / Year: 2002
Title: Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle.
Authors: Oubridge, C. / Kuglstatter, A. / Jovine, L. / Nagai, K.
History
DepositionMar 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: signal recognition particle RNA S domain
A: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,70727
Polymers51,9082
Non-polymers79925
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.765, 223.875, 43.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain signal recognition particle RNA S domain / SRP RNA / 7S RNA / 7SL RNA


Mass: 41566.715 Da / Num. of mol.: 1 / Mutation: C112G, G113A, G238U, G239C / Source method: obtained synthetically
Details: This sequence is 7SL RNA from Homo sapiens. 128 nt RNA fragment was in vitro transcribed under control of a T7 promoter with T7 RNA polymerase. It was Cotranscribed with 2 cis-acting ...Details: This sequence is 7SL RNA from Homo sapiens. 128 nt RNA fragment was in vitro transcribed under control of a T7 promoter with T7 RNA polymerase. It was Cotranscribed with 2 cis-acting hammerhead ribozymes to cleave homogeneous RNA from the full length transcript.
References: GenBank: 23932
#2: Protein SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN / SRP19


Mass: 10341.349 Da / Num. of mol.: 1 / Mutation: C61A, C63R, C80A, Q74C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: SRP19 / Plasmid: pRET3a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q58440
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MMC / METHYL MERCURY ION


Mass: 215.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.9 %
Description: ORIGINAL PHASES WERE DETERMINED BY SELENOMETHIONINE MAD BUT FINAL REFINEMENT WAS CARRIED OUT AGAINST A HIGHER QUALITY SINGLE WAVELENGTH DATASET FOR WHICH WE SUPPLY STATISTICS.
Crystal growTemperature: 300.5 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG4000, 110MM Tris.HCl pH 7.4, 10% glycerol, 50mm magnesium acetate, 100MM ammonium acetate, 5MM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K
Crystal grow
*PLUS
Temperature: 27.5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
2100 mMammonium acetate1drop
310 mMTris-HCl1droppH7.4
410 %glycerol1drop
55 mM1dropMgCl2
65 mMdithiothreitol1drop
712 %(w/v)PEG40001reservoir
80.1 MTris-HCl1reservoirpH7.4
950 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9185 / Wavelength: 0.9185 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 2.9→38 Å / Num. all: 29278 / Num. obs: 26760 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 114.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.1 / % possible all: 52.9
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 38 Å / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 52.9 % / Num. possible: 1544 / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
CNSrefinement
SHARPphasing
SOLOMONphasing
EDENmodel building
REFMACrefinement
SOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
EDENphasing
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→37.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 427207.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS/Refmac Dictionaries / Details: Refmac5.1 (Murshudov) was also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1228 5 %RANDOM
Rwork0.264 ---
all0.264 29278 --
obs0.264 24466 83.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.92 Å2 / ksol: 0.282066 e/Å3
Displacement parametersBiso mean: 98.2 Å2
Baniso -1Baniso -2Baniso -3
1-50.12 Å20 Å20 Å2
2---23.86 Å20 Å2
3----26.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.9→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 2706 26 30 3489
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.5
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it1.562
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 2.9→3.12 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.419 153 4.9 %
Rwork0.375 2941 -
obs--53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5LJ_PRO_010.PARAMLJ_PRO_010.TOP
X-RAY DIFFRACTION6LJ_RNA_010.PARAMLJ_RNA_010.TOP
Refinement
*PLUS
Rfactor obs: 0.264 / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Rfactor Rfree: 0.419 / Rfactor Rwork: 0.375

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