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- PDB-4uyk: Crystal structure of a Signal Recognition Particle Alu domain in ... -

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Basic information

Entry
Database: PDB / ID: 4uyk
TitleCrystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation
Components
  • SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
  • SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
  • SRP RNASignal recognition particle RNA
KeywordsSIGNALING PROTEIN / SIGNAL RECOGNITION PARTICLE / TRANSLATION / RNA / RNA FOLDING
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) / RNA (> 100) / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
PYROCOCCUS HORIKOSHII OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.22 Å
AuthorsBousset, L. / Mary, C. / Brooks, M.A. / Scherrer, A. / Strub, K. / Cusack, S.
CitationJournal: RNA / Year: 2014
Title: Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation.
Authors: Bousset, L. / Mary, C. / Brooks, M.A. / Scherrer, A. / Strub, K. / Cusack, S.
History
DepositionSep 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references

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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
R: SRP RNA


Theoretical massNumber of molelcules
Total (without water)66,1433
Polymers66,1433
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-48.6 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.860, 100.860, 197.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 10233.126 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEH9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49458
#2: Protein SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN / SRP14 / 18 KDA ALU RNA-BINDING PROTEIN


Mass: 12386.117 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEH14DELTAR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37108
#3: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 43523.797 Da / Num. of mol.: 1 / Fragment: ALU DOMAIN, RESIDUES 1-89 AND RESIDUES 289-314 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS HORIKOSHII OT3 (archaea) / References: GenBank: HG323574
Sequence detailsHUMAN SRP9 RESIDUES 1 TO 85 WERE EXPRESSED IN THIS WORK HUMAN SRP14 RESIDUES 1 TO 107 WERE ...HUMAN SRP9 RESIDUES 1 TO 85 WERE EXPRESSED IN THIS WORK HUMAN SRP14 RESIDUES 1 TO 107 WERE EXPRESSED IN THIS WORK THE P. HORIKOSHII SRP ALU RNA SEQUENCE HAS THE S-DOMAIN DELETED, AND REPLACED BY A TETRA LOOP. CCC (CYCLIC CYTIDINE), PRODUCED DURING IN-VITRO TRANSCRIPTION.

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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: 4.12 Å3/Da / Density % sol: 73.3 % / Description: NONE
Crystal growpH: 5
Details: 17.5% PEG 400, 5% GLYCEROL BUFFERED IN 100 MM SODIUM ACETATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2004
RadiationMonochromator: DIAMOND (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 30821 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 2.18 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.09
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 2.18 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.74 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.22→89.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 48.231 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23315 854 5 %RANDOM
Rwork0.1916 ---
obs0.19365 16238 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 123.705 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å20 Å2
2--3.44 Å20 Å2
3----6.89 Å2
Refinement stepCycle: LAST / Resolution: 3.22→89.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 2882 0 0 4259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0144624
X-RAY DIFFRACTIONr_bond_other_d0.0020.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.4786910
X-RAY DIFFRACTIONr_angle_other_deg1.07136462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82823.96658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.48415265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6311510
X-RAY DIFFRACTIONr_chiral_restr0.0720.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021049
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.796.421690
X-RAY DIFFRACTIONr_mcbond_other2.7886.419689
X-RAY DIFFRACTIONr_mcangle_it4.8169.598859
X-RAY DIFFRACTIONr_mcangle_other4.8139.602860
X-RAY DIFFRACTIONr_scbond_it2.527.3923934
X-RAY DIFFRACTIONr_scbond_other2.5197.3923935
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.18911.0686051
X-RAY DIFFRACTIONr_long_range_B_refined7.09171.3675914
X-RAY DIFFRACTIONr_long_range_B_other7.09171.3685915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.22→3.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 59 -
Rwork0.338 1136 -
obs--96.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0204-0.0338-0.1083.9951-1.07081.76510.067-0.05140.0489-0.1309-0.4436-0.8341-0.24350.81790.37660.4897-0.00160.05860.85570.00680.755793.968957.99979.2527
25.4347-1.784-2.07273.02531.09334.3278-0.1229-0.8320.1467-0.08760.73-0.21890.40750.0072-0.60710.57620.0649-0.11050.7538-0.24540.289889.282351.275512.3263
32.09980.16591.58370.72871.23743.36520.2997-0.360.08610.0555-0.1080.08130.5004-0.2427-0.19170.6040.0874-0.01550.69560.0270.381976.715643.78157.3572
42.5155-1.5530.81813.10191.54592.2616-0.1611-0.4413-0.05850.3480.08370.18760.3494-0.33950.07740.81350.07580.05830.84490.04010.132578.988646.828313.929
50.4647-0.8709-0.55161.68731.01880.817-0.0738-0.1026-0.0465-0.05280.25240.09080.08290.0631-0.17860.697-0.0422-0.02760.57380.01210.376481.686437.3684-12.4402
63.5925-0.77224.3450.2228-1.11316.55710.2060.4723-0.74380.2407-0.04930.0984-1.03790.9666-0.15681.60380.0731-0.5660.90070.21010.5646124.558130.71516.442
72.4602-2.0134-0.22862.08840.50750.56540.30620.06070.1972-0.4767-0.0479-0.2728-0.22330.3315-0.25830.6851-0.00620.08350.54830.01590.262683.958751.5996-21.0442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 25
2X-RAY DIFFRACTION2A26 - 82
3X-RAY DIFFRACTION3B1 - 42
4X-RAY DIFFRACTION4B50 - 97
5X-RAY DIFFRACTION5R6 - 85
6X-RAY DIFFRACTION6R86 - 117
7X-RAY DIFFRACTION7R118 - 139

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