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- PDB-3k0j: Crystal structure of the E. coli ThiM riboswitch in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3k0j
TitleCrystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module
Components
  • RNA (87-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA/RNA BINDING PROTEIN / riboswitch / RNA / thi-box / ThiM / U1A protein / Acetylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Ribonucleoprotein / RNA-binding / Spliceosome / RNA-RNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKulshina, N. / Edwards, T.E. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2010
Title: Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.
Authors: Kulshina, N. / Edwards, T.E. / Ferre-D'Amare, A.R.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U1 small nuclear ribonucleoprotein A
B: U1 small nuclear ribonucleoprotein A
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
E: RNA (87-MER)
F: RNA (87-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,40416
Polymers100,3596
Non-polymers1,04510
Water00
1
A: U1 small nuclear ribonucleoprotein A
C: U1 small nuclear ribonucleoprotein A
E: RNA (87-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,75110
Polymers50,1803
Non-polymers5717
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
F: RNA (87-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6536
Polymers50,1803
Non-polymers4743
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.250, 71.600, 128.350
Angle α, β, γ (deg.)90.00, 94.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A


Mass: 11079.939 Da / Num. of mol.: 4 / Fragment: UNP residues 2-97, RRM 1 domain / Mutation: Y231H,Q236R
Source method: isolated from a genetically manipulated source
Details: thiM RNA in vitro transcription / Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA, U1A protein / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#2: RNA chain RNA (87-MER)


Mass: 28019.666 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg

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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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 20% (v/v) PEG 550 MME, 20% MPD, and 80 mM sodium citrate (pH 5.6), VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: vertically collimating premirror, LN2 cooled double-crystal silicon (111) monochromator, toroidal focusing M2 mirror
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 17454 / Num. obs: 17359 / Redundancy: 4.4 % / Rsym value: 0.169 / Net I/σ(I): 9.3
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.556

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 65867.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1595 9.9 %RANDOM
Rwork0.197 ---
obs0.197 16145 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.1472 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.38 Å2-0 Å21.04 Å2
2--9.21 Å20 Å2
3----4.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 3642 60 0 6477
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.978
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.53
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.331.5
X-RAY DIFFRACTIONc_mcangle_it5.362
X-RAY DIFFRACTIONc_scbond_it4.762
X-RAY DIFFRACTIONc_scangle_it6.882.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 244 9.6 %
Rwork0.263 2306 -
obs--89 %
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
X-RAY DIFFRACTION5tpp_may16a.paramtpp_may16a.top

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