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- PDB-3tzr: Structure of a Riboswitch-like RNA-ligand complex from the Hepati... -

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Basic information

Entry
Database: PDB / ID: 3tzr
TitleStructure of a Riboswitch-like RNA-ligand complex from the Hepatitis C Virus Internal Ribosome Entry Site
Components
  • 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*CP*C)-3'
  • 5'-R(*GP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*GP*G)-3'
KeywordsRNA / internal loop / regulatory motif / aminobenzimidazole binding
Function / homologyChem-SS0 / RNA / RNA (> 10)
Function and homology information
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.212 Å
AuthorsDibrov, S.M. / Ding, K. / Brunn, N. / Parker, M.A. / Bergdahl, B.M. / Wyles, D.L. / Hermann, T.
CitationJournal: To be Published
Title: Structure of a Riboswitch in the Hepatitis C Virus Internal Ribosome Entry Site
Authors: Hermann, T. / Dibrov, S. / Ding, K. / Brunn, N. / Parker, M. / Bergdahl, M. / Wyles, D.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*CP*C)-3'
B: 5'-R(*GP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,23012
Polymers11,4652
Non-polymers76510
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-100 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.054, 33.582, 81.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*CP*C)-3'


Mass: 6319.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HCV IRES subdomain IIa chain A / Source: (synth.) Hepatitis C virus
#2: RNA chain 5'-R(*GP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*GP*G)-3'


Mass: 5145.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HCV IRES subdomain IIa chain B / Source: (synth.) Hepatitis C virus

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Non-polymers , 4 types, 91 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SS0 / (8R)-8-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-1,7,8,9-tetrahydrochromeno[5,6-d]imidazol-2-amine


Mass: 331.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N5O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.9 Å3/Da / Density % sol: 35.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM magnesium sulfate, 50 mM sodium cacodylate, 2.0 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 31, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→16.8 Å / Num. all: 4704 / Num. obs: 4664 / % possible obs: 99.15 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.35 / Redundancy: 6.7 %
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.5 % / % possible all: 75.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NOK

2nok


Resolution: 2.212→16.791 Å / SU ML: 0.83 / σ(F): 1.35 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 211 4.52 %
Rwork0.179 --
obs0.1815 4664 99.15 %
all-4704 -
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.079 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7418 Å2-0 Å20 Å2
2---2.4473 Å20 Å2
3---1.7055 Å2
Refinement stepCycle: LAST / Resolution: 2.212→16.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 757 45 81 883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006881
X-RAY DIFFRACTIONf_angle_d1.3131365
X-RAY DIFFRACTIONf_dihedral_angle_d16.89436
X-RAY DIFFRACTIONf_chiral_restr0.073179
X-RAY DIFFRACTIONf_plane_restr0.00737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2121-2.7850.3745960.23022160X-RAY DIFFRACTION98
2.785-16.79150.19581150.16152293X-RAY DIFFRACTION100

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