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- PDB-1jid: Human SRP19 in complex with helix 6 of Human SRP RNA -

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Basic information

Entry
Database: PDB / ID: 1jid
TitleHuman SRP19 in complex with helix 6 of Human SRP RNA
Components
  • HELIX 6 OF HUMAN SRP RNA
  • SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
KeywordsSIGNALING PROTEIN/RNA / SIGNAL RECOGNITION PARTICLE (SRP) / PROTEIN-RNA COMPLEX / GGAG TETRALOOP / SIGNALING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle / cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / nuclear body / nucleolus / RNA binding / cytosol
Similarity search - Function
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
: / RNA / RNA (> 10) / Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD with molecular replacement / Resolution: 1.8 Å
AuthorsWild, K. / Sinning, I. / Cusack, S.
Citation
Journal: Science / Year: 2001
Title: Crystal structure of an early protein-RNA assembly complex of the signal recognition particle.
Authors: Wild, K. / Sinning, I. / Cusack, S.
#1: Journal: Structure / Year: 1999
Title: The 2 A structure of helix 6 of the human signal recognition particle RNA
Authors: Wild, K. / Weichenrieder, O. / Leonard, G.A. / Cusack, S.
History
DepositionJul 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HELIX 6 OF HUMAN SRP RNA
A: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4684
Polymers24,4192
Non-polymers492
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.813, 109.782, 89.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe asymmetric unit contains one biological assembly

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Components

#1: RNA chain HELIX 6 OF HUMAN SRP RNA


Mass: 9628.433 Da / Num. of mol.: 1 / Mutation: C162U / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. The RNA has been in vitro transcribed using T7 RNA polymerase.
References: GenBank: 36086
#2: Protein SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN


Mass: 14791.062 Da / Num. of mol.: 1 / Fragment: 24 C-TERMINAL RESIDUES TRUNCATED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P09132
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.82 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: potassium chloride, magnesium chloride, sodium chloride, PEG 3350, isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MgCl211
3NaCl11
4PEG 335011
5isopropanol11
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMsodium citrate1reservoir
3450 mM1reservoirKCl
410 %PEG33501reservoir
51

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91902 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2001
RadiationMonochromator: Silicium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91902 Å / Relative weight: 1
ReflectionResolution: 1.8→49.75 Å / Num. all: 24024 / Num. obs: 23784 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 2.7 / % possible all: 61.2
Reflection shell
*PLUS
% possible obs: 61.2 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SHARPphasing
RefinementMethod to determine structure: SAD with molecular replacement
Starting model: PDB ENTRY 1D4R

1d4r


Resolution: 1.8→49.75 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1142 4.8 %RANDOM
Rwork0.186 ---
all-25876 --
obs-23740 91.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 65.4191 Å2 / ksol: 0.417491 e/Å3
Displacement parametersBiso mean: 27.63 Å2
Baniso -1Baniso -2Baniso -3
1-14.07 Å20 Å20 Å2
2---6.27 Å20 Å2
3----7.79 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 630 10 271 1828
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_improper_angle_d3.18
X-RAY DIFFRACTIONx_mcbond_it1.941.5
X-RAY DIFFRACTIONx_mcangle_it2.72
X-RAY DIFFRACTIONx_scbond_it2.432
X-RAY DIFFRACTIONx_scangle_it3.412.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
1.8-1.880.2621003.10.2619400.02663.9
1.88-1.980.2371364.30.23724270.0280.2
1.98-2.110.2051334.10.20628980.01894.5
2.11-2.270.18915950.1930450.01599.8
2.27-2.50.1721554.80.17230580.01499.8
2.5-2.860.1931594.90.19230760.01599.9
2.86-3.60.1791584.80.1830730.01499.1
3.6-49.750.1731424.20.17330810.01595
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna-allatom-mod.paramdna-rna-allatom-mod.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4mg3.parammg3.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg3.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.18
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / % reflection Rfree: 3.1 % / Rfactor Rwork: 0.26

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