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- PDB-1xnr: Crystal Structure of an Inosine-Cytosine Wobble Base Pair in the ... -

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Basic information

Entry
Database: PDB / ID: 1xnr
TitleCrystal Structure of an Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center
Components
  • (16S Ribosomal protein ...) x 20
  • 16S Ribosomal RNA
  • Anticodon tRNA
  • mRNA
KeywordsRIBOSOME / translation / decoding / 30S / tRNA modification
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain ...S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Ribosomal protein S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / S15/NS1, RNA-binding / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Few Secondary Structures / Irregular / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Nucleotidyltransferase; domain 5 / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily
Similarity search - Domain/homology
PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMurphy, F.V. / Ramakrishnan, V.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structure of a purine-purine wobble base pair in the decoding center of the ribosome.
Authors: Murphy, F.V. / Ramakrishnan, V.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Residues G1002 and G1003; G1031 and 1032; C1362 and A1363; C1539 and U1540 in chain A are ...SEQUENCE Residues G1002 and G1003; G1031 and 1032; C1362 and A1363; C1539 and U1540 in chain A are linked together which are shown as close contacts at remark 500. The missing residues within the links are listed in remark 465.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S Ribosomal RNA
X: Anticodon tRNA
W: mRNA
B: 16S Ribosomal protein S2
C: 16S Ribosomal protein S3
D: 16S Ribosomal protein S4
E: 16S Ribosomal protein S5
F: 16S Ribosomal protein S6
G: 16S Ribosomal protein S7
H: 16S Ribosomal protein S8
I: 16S Ribosomal protein S9
J: 16S Ribosomal protein S10
K: 16S Ribosomal protein S11
L: 16S Ribosomal protein S12
M: 16S Ribosomal protein S13
N: 16S Ribosomal protein S14
O: 16S Ribosomal protein S15
P: 16S Ribosomal protein S16
Q: 16S Ribosomal protein S17
R: 16S Ribosomal protein S18
S: 16S Ribosomal protein S19
T: 16S Ribosomal protein S20
V: 16S Ribosomal protein THX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)791,799134
Polymers788,42823
Non-polymers3,371111
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)401.122, 401.122, 175.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 3 types, 3 molecules AXW

#1: RNA chain 16S Ribosomal RNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076
#2: RNA chain Anticodon tRNA


Mass: 3506.155 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain mRNA


Mass: 1239.818 Da / Num. of mol.: 1 / Source method: obtained synthetically

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16S Ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV

#4: Protein 16S Ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371
#5: Protein 16S Ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80372
#6: Protein 16S Ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373
#7: Protein 16S Ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS
#8: Protein 16S Ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS
#9: Protein 16S Ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291
#10: Protein 16S Ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62668, UniProt: P0DOY9*PLUS
#11: Protein 16S Ribosomal protein S9


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80374
#12: Protein 16S Ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80375, UniProt: Q5SHN7*PLUS
#13: Protein 16S Ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80376
#14: Protein 16S Ribosomal protein S12


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 581812, UniProt: Q5SHN3*PLUS
#15: Protein 16S Ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80377
#16: Protein 16S Ribosomal protein S14


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24320, UniProt: P0DOY6*PLUS
#17: Protein 16S Ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80378, UniProt: Q5SJ76*PLUS
#18: Protein 16S Ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80379, UniProt: Q5SJH3*PLUS
#19: Protein 16S Ribosomal protein S17


Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62658, UniProt: P0DOY7*PLUS
#20: Protein 16S Ribosomal protein S18


Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS
#21: Protein 16S Ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS
#22: Protein 16S Ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80380
#23: Protein/peptide 16S Ribosomal protein THX


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62612, UniProt: Q5SIH3*PLUS

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Non-polymers , 3 types, 111 molecules

#24: 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
#25: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 108 / Source method: obtained synthetically / Formula: Mg
#26: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, magnesium chloride, potassium chloride, ammonium chloride, MES-KOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2magnesium chloride11
3potassium chloride11
4ammonium chloride11
5MES-KOH11
6H2O11
7MPD12
8magnesium chloride12
9potassium chloride12
10ammonium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.1→99 Å / Num. obs: 257063 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.2 % / Net I/σ(I): 14.35
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 2.54 / % possible all: 91.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: empty 30S

Resolution: 3.1→99 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 11896 set taken from starting model data
Rwork0.227 --
all0.235 --
obs0.235 235669 -
Displacement parametersBiso mean: 77.01 Å2
Refine analyze
FreeObs
Luzzati sigma a0.55 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.1→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19229 32694 152 0 52075
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_d1.207

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