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- PDB-3bnr: Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Dec... -

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Basic information

Entry
Database: PDB / ID: 3bnr
TitleCrystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)
Components(A site of human mitochondrial ribosome, chain ...) x 3
KeywordsRNA / ribosome / decoding site
Function / homology: / PAROMOMYCIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKondo, J. / Westhof, E.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Authors: Kondo, J. / Westhof, E.
History
DepositionDec 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_conn_type.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
A: A site of human mitochondrial ribosome, chain one
B: A site of human mitochondrial ribosome, chain two
C: A site of human mitochondrial ribosome, chain one
D: A site of human mitochondrial ribosome, chain three
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3527
Polymers28,6594
Non-polymers6943
Water3,297183
1
A: A site of human mitochondrial ribosome, chain one
B: A site of human mitochondrial ribosome, chain two
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5213
Polymers14,4822
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: A site of human mitochondrial ribosome, chain one
D: A site of human mitochondrial ribosome, chain three
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8314
Polymers14,1762
Non-polymers6552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.189, 77.380, 56.322
Angle α, β, γ (deg.)90.000, 115.120, 90.000
Int Tables number5
Space group name H-MC121

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Components

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A site of human mitochondrial ribosome, chain ... , 3 types, 4 molecules ACBD

#1: RNA chain A site of human mitochondrial ribosome, chain one


Mass: 7394.280 Da / Num. of mol.: 2 / Mutation: A1555G / Source method: obtained synthetically
#2: RNA chain A site of human mitochondrial ribosome, chain two


Mass: 7088.115 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically
#3: RNA chain A site of human mitochondrial ribosome, chain three


Mass: 6781.949 Da / Num. of mol.: 1 / Mutation: A1555G / Source method: obtained synthetically

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Non-polymers , 3 types, 186 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, KCl, spermine tetrachloride, paromomycin, 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3Sodium cacodylate11
4MPD12
5KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91625 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91625 Å / Relative weight: 1
ReflectionResolution: 2.1→50.995 Å / Num. obs: 16388 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 2.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.217.10.3781.51667923590.378100
2.21-2.357.10.2762.41607222770.276100
2.35-2.5170.20231496321310.202100
2.51-2.7170.1553.31379119700.155100
2.71-2.976.90.1223.61273118400.122100
2.97-3.326.80.1093.21120816420.10999.9
3.32-3.836.70.1143.2984414640.11499.9
3.83-4.76.50.1084.6797812210.10899.1
4.7-6.646.20.0925.859769630.09299.8
6.64-50.996.30.089632895210.08996

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50.995 Å / FOM work R set: 0.828 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.245 1609 9.9 %
Rwork0.215 --
obs-16147 99.7 %
Solvent computationBsol: 69.092 Å2
Displacement parametersBiso mean: 36.922 Å2
Baniso -1Baniso -2Baniso -3
1--5.934 Å20 Å2-7.116 Å2
2--10.754 Å20 Å2
3----4.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1892 44 183 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0041.5
X-RAY DIFFRACTIONc_angle_deg0.92
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1rna_free.param
X-RAY DIFFRACTION2bru.param
X-RAY DIFFRACTION3par2_xplor.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

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