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- PDB-1e8o: Core of the Alu domain of the mammalian SRP -

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Basic information

Entry
Database: PDB / ID: 1e8o
TitleCore of the Alu domain of the mammalian SRP
Components
  • 7SL RNA
  • SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
  • SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
KeywordsALU RIBONUCLEOPROTEIN PARTICLE / PROTEIN RECOGNITION OF AN RNA U-TURN / TRANSLATIONAL CONTROL / ALU RNP ASSEMBLY AND TRANSPORT / 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 alu RNA binding heterodimer, srp9/1 / 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 alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
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 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
D: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
E: 7SL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7878
Polymers60,4995
Non-polymers2883
Water39622
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-33.8 kcal/mol
Surface area27790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.448, 186.621, 189.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

DetailsTHE BIOLOGICALLY RELEVANT TERNARY COMPLEX CONSISTS OF CHAINSC,D AND E. THE SRP9/14 HETERODIMER FORMED BY CHAINS A AND BIS BOUND NON -SPECIFICALLY.

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Components

#1: Protein SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN / SRP9


Mass: 9996.567 Da / Num. of mol.: 2
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


Mass: 12114.235 Da / Num. of mol.: 2 / 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


Mass: 16277.622 Da / Num. of mol.: 1 / Fragment: ALU RNA 5' DOMAIN / 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) / References: EMBL: X01037
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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 A CONTAINS ENGINEERED MUTATION U119C

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 71 %
Crystal growpH: 5
Details: 50MM NAOAC, 10MM MGCL2, 140MM NACL, 390MM (NH4)2SO4, 21% PEG2000, pH 5.00
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: vapor diffusion, hanging drop / pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.130 mMSA501drop
20.180 mMSRP9/141drop
32.5 mMHEPES1droppH7.5
425 mMsodium acetate1droppH5.0
510 mM1dropMgCl2
675 mM1dropNaCl
7210 mMammonium sulfate1drop
85 mMdithiothreitol1drop
911 %PEG20001drop
1050 mMsodium acetate1reservoirpH5.0
1110 mM1reservoirMgCl2
12140 mM1reservoirNaCl
13390 mMammonium sulfate1reservoir
1421 %PEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.784
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.784 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 16328 / % possible obs: 94.9 % / Redundancy: 2.4 % / Biso Wilson estimate: 67.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 5.6
Reflection shellResolution: 3.22→3.35 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.468 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMV. 6.0data reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1914, MODIFIED

Resolution: 3.2→47.46 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2572751.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 829 5.1 %RANDOM
Rwork0.245 ---
obs0.245 16328 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45 Å2 / ksol: 0.266247 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å20 Å20 Å2
2--6.15 Å20 Å2
3----2.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.2→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 1079 15 22 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.982.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 128 5 %
Rwork0.322 2439 -
obs--90.8 %
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.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.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_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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