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- PDB-1e8s: Alu domain of the mammalian SRP (potential Alu retroposition inte... -

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Basic information

Entry
Database: PDB / ID: 1e8s
TitleAlu domain of the mammalian SRP (potential Alu retroposition intermediate)
Components
  • 7SL RNA, 88-MER
  • SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
  • SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
KeywordsALU RIBONUCLEOPROTEIN PARTICLE / ALU RNP ASSEMBLY AND DIMERISATION / TRANSLATIONAL CONTROL / ALU RETROPOSITION
Function / homology
Function and homology information


signal recognition particle receptor complex / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / negative regulation of translational elongation / cotranslational protein targeting to membrane / protein targeting to ER / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane ...signal recognition particle receptor complex / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / negative regulation of translational elongation / cotranslational protein targeting to membrane / protein targeting to ER / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / RNA binding / extracellular region / nucleus / 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
Similarity search - Domain/homology
EUROPIUM (III) ION / RNA / RNA (> 10) / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B ; P ATOMS ONLY, CHAIN C
AuthorsWeichenrieder, O. / Wild, K. / Strub, K. / Cusack, S.
CitationJournal: Nature / Year: 2000
Title: Structure and Assembly of the Alu Domain of the Mammalian Signal Recognition Particle
Authors: Weichenrieder, O. / Wild, K. / Strub, K. / Cusack, S.
History
DepositionSep 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
B: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
C: 7SL RNA, 88-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9065
Polymers50,6023
Non-polymers3042
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)143.330, 143.330, 60.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN / SRP9 / Coordinate model: Cα atoms only


Mass: 9996.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASM, NUCLEUS? / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49458
#2: Protein SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN / SRP14 / Coordinate model: Cα atoms only


Mass: 12114.235 Da / Num. of mol.: 1 / Fragment: TRUNCATED AFTER K107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASM, NUCLEUS? / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37108
#3: RNA chain 7SL RNA, 88-MER / Coordinate model: P atoms only


Mass: 28490.900 Da / Num. of mol.: 1 / Fragment: ALU RNA / Mutation: YES / Source method: obtained synthetically
Details: THE RNA WAS PRODUCED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE USING RIBOZYME TECHNOLOGY.
Source: (synth.) HOMO SAPIENS (human)
#4: Chemical ChemComp-EU3 / EUROPIUM (III) ION / Europium


Mass: 151.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Eu
Compound detailsSIGNAL-RECOGNITION-PARTICLE ASSEMBLY HAS A CRUCIAL ROLE IN TARGETING SECRETORY PROTEINS TO THE ...SIGNAL-RECOGNITION-PARTICLE ASSEMBLY HAS A CRUCIAL ROLE IN TARGETING SECRETORY PROTEINS TO THE ROUGH ENDOPLASMIC RETICULUM MEMBRANE. SRP9 TOGETHER WITH SRP14 AND THE ALU PORTION OF THE SRP RNA, CONSTITUTES THE ELONGATION ARREST DOMAIN OF SRP. THE COMPLEX OF SRP9 AND SRP14 IS REQUIRED FOR SRP RNA BINDING. SIGNAL RECOGNITION PARTICLE CONSISTS OF A 7S RNA MOLECULE OF 300 NUCLEOTIDES AND SIX PROTEIN SUBUNITS: SRP72, SRP68, SRP54, SRP19, SRP14 AND SRP9. CHAIN C CONTAINS ENGINEERED MUTATIONS U119C, C152U, U153G

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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: 3.06 Å3/Da / Density % sol: 66 % / Description: EUROPIUM L(III) EDGE
Crystal growpH: 7
Details: 50MM HEPES, 10MM MGCL2, 150MM NACL, 0.8 MM EU(NO3)3, 390MM (NH4)2SO4, 23% PEG400, pH 7.00
Crystal
*PLUS
Density % sol: 67 %
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.070 mMSA88 RNP1drop
228 mMHEPES1droppH7.0
310 mM1dropMgCl2
475 mM1dropNaCl
50.40 mMEu(NO3)31drop
65 mMdithiothreitol1drop
7210 mMammonium sulfate1drop
812 %PEG4001drop
950 mMHEPES1reservoir
1010 mM1reservoirpH7.0MgCl2
11150 mM1reservoirNaCl
120.80 mMEu(NO3)31reservoir
13390 mMammonium sulfate1reservoir
1423 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.7757,1.7753,1.033,0.9326
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.77571
21.77531
31.0331
40.93261
ReflectionResolution: 4→50 Å / Num. obs: 5053 / % possible obs: 90.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 211.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 5.9
Reflection shellResolution: 4→4.1 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.541 / % possible all: 59.6

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Processing

Software
NameVersionClassification
HKLdata reduction
MOSFLMV. 6.0data reduction
HKLdata scaling
SCALAdata scaling
SHARPphasing
SOLOMONphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 4→37.46 Å / Data cutoff high absF: 3024867.55 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.388 --
obs0.388 5448 96.2 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 15 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1--6.33141 Å20 Å20 Å2
2---6.33141 Å20 Å2
3---12.6628 Å2
Refinement stepCycle: LAST / Resolution: 4→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms147 86 2 0 235
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.44
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
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 DIFFRACTION3ION_EU.PARAMION-EU.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.44

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