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

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Basic information

Entry
Database: PDB / ID: 4uyj
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 RNA
KeywordsSIGNALING PROTEIN / SIGNAL RECOGNITION PARTICLE / TRANSLATION / 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 / cotranslational protein targeting to membrane / protein targeting to ER / negative regulation of translational elongation / 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 / cotranslational protein targeting to membrane / protein targeting to ER / negative regulation of translational elongation / 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 / MOLECULAR REPLACEMENT / Resolution: 3.35 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
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
R: SRP RNA
S: SRP RNA


Theoretical massNumber of molelcules
Total (without water)116,5596
Polymers116,5596
Non-polymers00
Water00
1
C: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
D: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
S: SRP RNA


Theoretical massNumber of molelcules
Total (without water)58,2793
Polymers58,2793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-47 kcal/mol
Surface area23620 Å2
MethodPISA
2
A: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
B: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
R: SRP RNA


Theoretical massNumber of molelcules
Total (without water)58,2793
Polymers58,2793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-46.2 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.950, 108.600, 128.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 10233.126 Da / Num. of mol.: 2 / 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.: 2 / 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


Mass: 35660.113 Da / Num. of mol.: 2 / Fragment: ALU DOMAIN, RESIDUES 1-89 AND RESIDUES 289-314 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS HORIKOSHII OT3 (archaea) / References: GenBank: HG323574
Has protein modificationY
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. THE 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: 2.97 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 4.6
Details: 17.5% PEG 3350, 2.5% GLYCEROL, 0.3 M AMMONIUM SULPHATE AND 0.1 M SODIUM ACETATE AT PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2004 / Details: MIRRORS
RadiationMonochromator: SINGLE SILICON (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 21235 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.026 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.21
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 3.98 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.85 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SRP914 ALU134 MODEL

Resolution: 3.35→82.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.841 / SU B: 65.401 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23643 1087 5.1 %RANDOM
Rwork0.19229 ---
obs0.19455 20150 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.935 Å2
Baniso -1Baniso -2Baniso -3
1--8.63 Å20 Å20 Å2
2---2.08 Å20 Å2
3---10.7 Å2
Refinement stepCycle: LAST / Resolution: 3.35→82.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 4722 0 0 7244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0147846
X-RAY DIFFRACTIONr_bond_other_d0.0020.024739
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.49611679
X-RAY DIFFRACTIONr_angle_other_deg1.014311173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21424110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70815484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8371518
X-RAY DIFFRACTIONr_chiral_restr0.0650.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021789
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_it1.8877.6291256
X-RAY DIFFRACTIONr_mcbond_other1.8787.6291255
X-RAY DIFFRACTIONr_mcangle_it3.19911.441563
X-RAY DIFFRACTIONr_mcangle_other3.19911.4391564
X-RAY DIFFRACTIONr_scbond_it1.7197.4026590
X-RAY DIFFRACTIONr_scbond_other1.7187.4026591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.86911.07910117
X-RAY DIFFRACTIONr_long_range_B_refined4.76571.55210002
X-RAY DIFFRACTIONr_long_range_B_other4.76571.55310003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.354→3.441 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 81 -
Rwork0.365 1396 -
obs--95.41 %
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)
18.4693.5534-2.19037.86283.201810.77070.16090.35760.09770.48830.0882-1.6158-0.25630.7829-0.24910.3184-0.0056-0.10270.4228-0.03980.951725.341237.1036.2302
21.6607-1.36480.32883.5923-0.04928.47720.0312-0.12660.02950.93490.038-1.0821-0.04750.2254-0.06920.5893-0.0759-0.21640.5288-0.03240.63118.939239.245114.0716
34.2171-4.00282.56926.8184-0.18313.69640.0782-0.3514-0.20780.06240.02940.2072-0.2457-0.8121-0.10770.703-0.09180.01970.67910.00960.34235.286245.949812.4171
48.66781.51721.12624.5882-2.36496.623-0.0350.03390.9420.2365-0.1709-0.1436-0.68270.59960.20590.73660.0473-0.08920.3294-0.08260.237910.671549.76912.0334
50.8859-0.92961.39191.3571-2.15046.1919-0.18950.1844-0.01560.28110.0437-0.1737-0.3640.8210.14580.16710.020.0560.543-0.10840.642440.434987.46172.9164
63.85292.12952.61584.0469-2.739511.45190.02250.3366-0.44050.73540.1422-0.9618-0.53520.9652-0.16470.3060.1423-0.16880.2107-0.07930.77835.539589.449511.597
74.5154-0.94013.89679.4204-2.46029.86-0.1766-0.0367-0.27340.66950.36610.0445-0.5914-0.6436-0.18950.0790.0458-0.01560.11290.04430.081722.547497.113712.6303
86.8904-0.14963.61559.4733-2.19619.88010.15160.16720.60990.8399-0.1644-0.6384-0.73720.85660.01280.25650.0337-0.07820.1728-0.06060.232128.184599.912311.9718
94.0098-3.21933.58473.2527-2.67423.49690.5056-0.334-0.8843-0.1880.24630.61050.2282-0.3616-0.75190.525-0.0539-0.11970.23330.08410.2632-2.282726.28432.2197
104.554-3.22592.12224.2739-2.40871.88850.23730.0375-1.1257-0.1490.27550.60520.3695-0.2676-0.51280.209-0.1037-0.1130.1261-0.00070.314812.05878.941.9853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 25
2X-RAY DIFFRACTION2A26 - 75
3X-RAY DIFFRACTION3B1 - 39
4X-RAY DIFFRACTION4B51 - 93
5X-RAY DIFFRACTION5C2 - 25
6X-RAY DIFFRACTION6C26 - 75
7X-RAY DIFFRACTION7D1 - 39
8X-RAY DIFFRACTION8D51 - 94
9X-RAY DIFFRACTION9R6 - 115
10X-RAY DIFFRACTION10S6 - 115

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