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- PDB-3cun: Aminoacyl-tRNA synthetase ribozyme -

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Basic information

Entry
Database: PDB / ID: 3cun
TitleAminoacyl-tRNA synthetase ribozyme
Components
  • RNA (92-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA/RNA binding / ARS ribozyme catalytic RNA / RNA-RNA binding 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
: / : / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsXiao, H. / Murakami, H. / Suga, H. / Ferre-D'Amare, A.R.
CitationJournal: Nature / Year: 2008
Title: Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme.
Authors: Xiao, H. / Murakami, H. / Suga, H. / Ferre-D'Amare, A.R.
History
DepositionApr 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (92-MER)
D: RNA (92-MER)
A: U1 small nuclear ribonucleoprotein A
B: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,10715
Polymers82,7914
Non-polymers31711
Water0
1
C: RNA (92-MER)
A: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5568
Polymers41,3952
Non-polymers1616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RNA (92-MER)
B: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5517
Polymers41,3952
Non-polymers1565
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.368, 48.076, 90.645
Angle α, β, γ (deg.)90.00, 93.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (92-MER)


Mass: 29820.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Flexizyme / Production host: CELL-FREE SYNTHESIS (others)
#2: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A


Mass: 11574.792 Da / Num. of mol.: 2 / Fragment: UNP residues 1-98 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co

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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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 100 mM magenesium formate pH 7.0, 15% PEG 3000, 1 M lithium chloride, VAPOR DIFFUSION, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium formate11
2magnesium formate12
3PEG 300012
4lithium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9572 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2005 / Details: Si (111)
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9572 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 13610 / % possible obs: 80.8 % / Observed criterion σ(I): 1.9 / Redundancy: 6.4 % / Rmerge(I) obs: 0.87 / Rsym value: 0.87 / Net I/σ(I): 21.1
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1355 / Rsym value: 0.501 / % possible all: 51.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3CUL

3cul


Resolution: 3→28.75 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 185743.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1355 10 %RANDOM
Rwork0.252 ---
all0.252 ---
obs0.252 13610 80.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 100.7 Å2
Baniso -1Baniso -2Baniso -3
1--40.72 Å20 Å2-1 Å2
2--35.4 Å20 Å2
3---5.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 3946 11 0 5364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d12.4
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_mcangle_it3.292
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 114 10.7 %
Rwork0.379 954 -
obs--38.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5gtn.paramgtn.top

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