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- PDB-1lng: Crystal Structure of the SRP19-7S.S SRP RNA Complex of M. jannaschii -

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Basic information

Entry
Database: PDB / ID: 1lng
TitleCrystal Structure of the SRP19-7S.S SRP RNA Complex of M. jannaschii
Components
  • 7S.S SRP RNA
  • Signal recognition particle 19 kDa protein
KeywordsSIGNALING PROTEIN/RNA / Protein-RNA complex / SIGNALING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane
Similarity search - Function
Signal recognition particle, SRP19 subunit, archaeal-type / 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 speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
CitationJournal: Nature / Year: 2002
Title: Structure of the SRP19 RNA complex and implications for signal recognition particle assembly.
Authors: Hainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.5Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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.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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 7S.S SRP RNA
A: Signal recognition particle 19 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8544
Polymers41,8052
Non-polymers492
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.521, 61.405, 155.978
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: RNA chain 7S.S SRP RNA


Mass: 31428.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Description: in vitro transcription
#2: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 10376.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: Q58440
#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.: 208 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, HEPES, MgAc, CaCl, DMSO, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2HEPES11
3MgAc11
4CaCl11
5DMSO11
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
2250 mM1dropKCl
31 %beta-mercaptoethanol1drop
45 %glycerol1drop
53 mg/mlprotein1drop
65 mM1dropMgCl2
70.1 MHEPES1reservoirpH7.0
80.1 Mmagnesium acetate1reservoir
90.02 M1reservoirCaCl2
105 %dimethylsulphoxide1reservoir
1118 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.12 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 18606 / Num. obs: 18606 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.099
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.332 / % possible all: 91
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 78892 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 91 % / Rmerge(I) obs: 0.332

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Processing

Software
NameVersionClassification
REFMAC5refinement
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1D4R and 1DUL

1d4r

1dul


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.098 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27333 955 5.1 %RANDOM
Rwork0.22444 ---
all0.22697 18606 --
obs0.22697 17651 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.347 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å20 Å2
2--2.18 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 2080 10 200 3017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213075
X-RAY DIFFRACTIONr_angle_refined_deg2.7042.7884628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.917386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.29415174
X-RAY DIFFRACTIONr_chiral_restr0.090.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021540
X-RAY DIFFRACTIONr_nbd_refined0.2730.31434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.5307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.511
X-RAY DIFFRACTIONr_mcbond_it0.8261.5435
X-RAY DIFFRACTIONr_mcangle_it1.5982705
X-RAY DIFFRACTIONr_scbond_it1.68432640
X-RAY DIFFRACTIONr_scangle_it2.5394.53923
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 68
Rwork0.245 1194
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)
10.6047-0.1131-0.12551.2217-0.22360.69230.047-0.0043-0.0402-0.0369-0.00430.0634-0.0041-0.0422-0.04270.28850.006-0.01150.2493-0.00490.370616.3583-9.466434.9391
23.1869-1.2552.73140.6394-2.31486.7911-0.3703-0.2321-0.0403-0.42710.0993-0.2539-0.607-0.4760.27090.6288-0.0151-0.04130.2949-0.11180.171328.5041-3.563695.3851
34.3689-1.47491.61623.48-1.08314.3823-0.1599-0.0157-0.28080.3397-0.1936-0.2206-0.32720.95570.35350.219-0.0713-0.00760.55460.1160.024533.995-4.103479.9917
40.8089-0.40150.26030.8044-0.5647-0.1932-0.0673-0.16550.10750.16950.0501-0.0159-0.1041-0.07840.01720.33440.0011-0.0140.3237-0.04250.324318.53183.845156.2306
50.910.06330.05150.29830.0562-0.89570.0824-0.2183-0.016-0.0120.04430.0077-0.0650.0968-0.12670.31230.00180.01260.35020.00450.314836.0895-3.050349.9714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB1 - 871 - 87
2X-RAY DIFFRACTION2BA140 - 1481 - 9
3X-RAY DIFFRACTION2BA233 - 23694 - 97
4X-RAY DIFFRACTION3BA182 - 19843 - 59
5X-RAY DIFFRACTION3BA226 - 23287 - 93
6X-RAY DIFFRACTION4BA149 - 18110 - 42
7X-RAY DIFFRACTION5BA199 - 22560 - 86
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor all: 0.22697 / Rfactor obs: 0.225 / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.305 / Rfactor Rwork: 0.245 / Rfactor obs: 0.245

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