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- PDB-1mms: Crystal structure of the ribosomal PROTEIN L11-RNA complex -

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Basic information

Entry
Database: PDB / ID: 1mms
TitleCrystal structure of the ribosomal PROTEIN L11-RNA complex
Components
  • 23S RIBOSOMAL RNA
  • PROTEIN (RIBOSOMAL PROTEIN L11)
KeywordsRIBOSOME / RNA-PROTEIN COMPLEX / RNA / TRANSLOCATION / THIOSTREPTON
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily ...Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / METHYL MERCURY ION / RNA / RNA (> 10) / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.57 Å
AuthorsWimberly, B.T. / Guymon, R. / Mccutcheon, J.P. / White, S.W. / Ramakrishnan, V.
Citation
Journal: Cell / Year: 1999
Title: A detailed view of a ribosomal active site: the structure of the L11-RNA complex.
Authors: B T Wimberly / R Guymon / J P McCutcheon / S W White / V Ramakrishnan /
Abstract: We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton ...We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor function. The highly compact RNA has both familiar and novel structural motifs. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. These antibiotics are proposed to bind in this cleft, locking the putative switch and interfering with the function of elongation factors.
#1: Journal: Biochemistry / Year: 1996
Title: Cooperative interactions of RNA and thiostrepton antibiotic with two domains of ribosomal protein L11.
Authors: Xing, Y. / Draper, D.E.
#2: Journal: J.Biol.Chem. / Year: 1982
Title: Site of action of a ribosomal RNA methylase conferring resistance to thiostrepton.
Authors: Thompson, J. / Schmidt, F. / Cundliffe, E.
#3: Journal: Eur.J.Biochem. / Year: 1979
Title: Binding of thiostrepton to a complex of 23-S rRNA with ribosomal protein L11.
Authors: Thompson, J. / Cundliffe, E. / Stark, M.
History
DepositionApr 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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
C: 23S RIBOSOMAL RNA
D: 23S RIBOSOMAL RNA
A: PROTEIN (RIBOSOMAL PROTEIN L11)
B: PROTEIN (RIBOSOMAL PROTEIN L11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,43439
Polymers67,3484
Non-polymers3,08635
Water2,558142
1
C: 23S RIBOSOMAL RNA
A: PROTEIN (RIBOSOMAL PROTEIN L11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,55722
Polymers33,6742
Non-polymers1,88320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 23S RIBOSOMAL RNA
B: PROTEIN (RIBOSOMAL PROTEIN L11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,87717
Polymers33,6742
Non-polymers1,20315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.890, 84.260, 155.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.974505, 0.101458, -0.200117), (0.097433, -0.994793, -0.029885), (-0.202107, 0.009626, -0.979316)-4.5433, -3.7488, -50.6929
2given(0.973477, 0.09878, -0.206364), (0.098758, -0.995057, -0.010432), (-0.206374, -0.010225, -0.97842)-4.8963, -2.8905, -50.9724

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Components

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RNA chain / Protein , 2 types, 4 molecules CDAB

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 18693.145 Da / Num. of mol.: 2 / Fragment: RESIDUES 1051-1108 / Mutation: U1108C / Source method: obtained synthetically / Details: IN VITRO TRANSCRIBED RRNA FROM THERMOTOGA MARITIMA
#2: Protein PROTEIN (RIBOSOMAL PROTEIN L11)


Mass: 14980.726 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT MERCURY LIGAND AT CYS39 / Source: (gene. exp.) Thermotoga maritima (bacteria) / Description: RECOMBINANT PROTEIN / Plasmid: PET13A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29395

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Non-polymers , 4 types, 177 molecules

#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-MMC / METHYL MERCURY ION / Methylmercury


Mass: 215.625 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH3Hg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHERE ARE A TOTAL OF 8 METHYLMERCURY IONS IN THE STRUCTURE. THE METHYL GROUP HAS NOT BEEN MODELLED ...THERE ARE A TOTAL OF 8 METHYLMERCURY IONS IN THE STRUCTURE. THE METHYL GROUP HAS NOT BEEN MODELLED FOR ANY OF THESE IONS. TWO OF THE IONS ARE COVALENTLY BOUND TO CYS A 39. ONE IS COVALENTLY BOUND TO U C 1061. ONE IS COVALENTLY BOUND TO U D 1061.

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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: 55 % / Description: TWO WAVELENGTH HG MAD
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 25% GLYCEROL, 15% PEG 4000, 50 MM TRIS PH 7.5, 50 MM MGCL2, 20 MM CDCL2, 0.2 M KCL, 1 MM DITHIOTHREITOL, 4 DEGREES C, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1GLYCEROL11
2PEG 400011
3TRIS11
4MGCL211
5CDCL211
6KCL11
7DITHIOTHREITOL11
8PEG 400012
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.15 mMprotein1drop
225 %glycerol1reservoir
315 %PEG40001reservoir
40.2 M1reservoirKCl
550 mM1reservoirMgCl2
620 mM1reservoirCdCl2
71 mMdithiothreitol1reservoir
850 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.980,1.010
DetectorType: BRANDEIS / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.011
ReflectionResolution: 2.57→20 Å / Num. all: 49313 / Num. obs: 49313 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 58.8 Å2 / Rsym value: 0.041 / Net I/σ(I): 20
Reflection shellResolution: 2.57→2.73 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.17 / % possible all: 86.2
Reflection
*PLUS

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.57→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS RESTRAINTS APPLIED TO RNA THROUGHOUT, NOT TO PROTEIN THE ASYMMETRIC UNIT CONTAINS TWO L11-RNA COMPLEXES. COMPLEX 1 CONSISTS OF CHAINS A AND C, AND COMPLEX 2 CONSISTS OF CHAINS B AND D. ...Details: NCS RESTRAINTS APPLIED TO RNA THROUGHOUT, NOT TO PROTEIN THE ASYMMETRIC UNIT CONTAINS TWO L11-RNA COMPLEXES. COMPLEX 1 CONSISTS OF CHAINS A AND C, AND COMPLEX 2 CONSISTS OF CHAINS B AND D. RESIDUES 1-7 AND 141 OF CHAIN A ARE DISORDERED. THE DENSITY FOR RESIDUES 8-70 OF CHAIN A WAS OF SIGNIFICANTLY LOWER QUALITY THAN THE DENSITY FOR THE REMAINDER OF THE ASYMMETRIC UNIT, AND THE QUALITY OF THE MODEL FOR THIS N-TERMINAL DOMAIN IS LOWER THAN THAT OF THE C-TERMINAL DOMAIN (RESIDUES 71-140). RESIDUES 1-70 AND 141 OF CHAIN B ARE DISORDERED. THE RNA IS NUMBERED WITH THE E. COLI NUMBERING TO FACILITATE COMPARISON WITH THE EXTENSIVE BIOCHEMICAL DATA ON THE E. COLI RNA-L11 SYSTEM. THE E. COLI RNA NUMBERING IS ALSO USED IN THE PRIMARY REFERENCE DESCRIBING THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2398 4.9 %RANDOM
Rwork0.219 ---
all-49313 --
obs-49313 95.5 %-
Displacement parametersBiso mean: 42.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 2474 35 142 4173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.591.5
X-RAY DIFFRACTIONx_mcangle_it5.282
X-RAY DIFFRACTIONx_scbond_it6.592
X-RAY DIFFRACTIONx_scangle_it9.242.5
Refine LS restraints NCS

NCS model details: RESTRAINTS / Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 5.51 Å2 / Rms dev position: 0.07 Å / Weight Biso : 2 / Weight position: 50

Ens-IDDom-IDAuth asym-ID
11C
22D
LS refinement shellResolution: 2.57→2.73 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.432 331 4.5 %
Rwork0.386 7101 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION2PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.432 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.386

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