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- PDB-1zho: The structure of a ribosomal protein L1 in complex with mRNA -

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Basic information

Entry
Database: PDB / ID: 1zho
TitleThe structure of a ribosomal protein L1 in complex with mRNA
Components
  • 50S ribosomal protein L1
  • mRNAMessenger RNA
KeywordsSTRUCTURAL PROTEIN/RNA / RIBOSOME / RIBOSOMAL PROTEIN / MRNA-PROTEIN COMPLEX / L1 / REGULATION OF GENE EXPRESSION / RNA-PROTEIN INTERACTION / STRUCTURAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein ...Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNevskaya, N. / Tishchenko, S. / Volchkov, S. / Kljashtorny, V. / Nikonova, E. / Nikonov, O. / Nikulin, A. / Kohrer, C. / Piendl, W. / Zimmermann, R. ...Nevskaya, N. / Tishchenko, S. / Volchkov, S. / Kljashtorny, V. / Nikonova, E. / Nikonov, O. / Nikulin, A. / Kohrer, C. / Piendl, W. / Zimmermann, R. / Stockley, P. / Garber, M. / Nikonov, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: New insights into the interaction of ribosomal protein L1 with RNA.
Authors: Nevskaya, N. / Tishchenko, S. / Volchkov, S. / Kljashtorny, V. / Nikonova, E. / Nikonov, O. / Nikulin, A. / Kohrer, C. / Piendl, W. / Zimmermann, R. / Stockley, P. / Garber, M. / Nikonov, S.
History
DepositionApr 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / 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_asym_id / _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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: mRNA
D: mRNA
F: mRNA
H: mRNA
A: 50S ribosomal protein L1
C: 50S ribosomal protein L1
E: 50S ribosomal protein L1
G: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,74712
Polymers148,5908
Non-polymers1564
Water5,026279
1
B: mRNA
A: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1873
Polymers37,1482
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: mRNA
C: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1873
Polymers37,1482
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: mRNA
E: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1873
Polymers37,1482
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: mRNA
G: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1873
Polymers37,1482
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.600, 101.900, 119.600
Angle α, β, γ (deg.)90.00, 93.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain
mRNA / Messenger RNA


Mass: 12270.358 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: SYNTHESIS OF THE RNA FRAGMENT FROM THE PLASMID PUC18, SEQUENCE FROM CELL-FREE (IN VITRO) SYSTEM WITHOUT LIVING ORGANISM
#2: Protein
50S ribosomal protein L1 /


Mass: 24877.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplA, rpl1 / Plasmid: pACA-L1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P27150
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.1 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MgCl211
3HgCl211
4PEG 1000011
5cacodylateCacodylic acid11
6glycerol11
7H2O11
8KCl12
9MgCl212
10HgCl212
11PEG 1000012
12cacodylateCacodylic acid12
13H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→37.06 Å / Num. all: 52853 / Num. obs: 50877 / % possible obs: 96.3 % / Biso Wilson estimate: 48.7 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U63, 1AD2

1u63

1ad2


Resolution: 2.6→37.06 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2374422.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2393 5 %RANDOM
Rwork0.218 ---
obs0.218 47974 90.7 %-
all-52853 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7713 Å2 / ksol: 0.296212 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å2-10.85 Å2
2---0.9 Å20 Å2
3----1.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.6→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6968 3264 4 279 10515
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.5
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_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 343 4.6 %
Rwork0.35 7040 -
obs--84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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