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- PDB-3r1h: Crystal structure of the Class I ligase ribozyme-substrate prelig... -

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Basic information

Entry
Database: PDB / ID: 3r1h
TitleCrystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Ca2+ bound
Components
  • 5'-R(*UP*CP*CP*AP*GP*UP*A)-3'
  • Class I ligase ribozyme
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN/RNA / ligase ribozyme / catalytic RNA / ribozyme / RNA BINDING PROTEIN-RNA 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) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsShechner, D.M. / Bartel, D.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: The structural basis of RNA-catalyzed RNA polymerization.
Authors: Shechner, D.M. / Bartel, D.P.
History
DepositionMar 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 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_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.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_ref_seq_dif.details / _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: U1 small nuclear ribonucleoprotein A
B: 5'-R(*UP*CP*CP*AP*GP*UP*A)-3'
C: Class I ligase ribozyme
D: U1 small nuclear ribonucleoprotein A
E: 5'-R(*UP*CP*CP*AP*GP*UP*A)-3'
F: Class I ligase ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,29132
Polymers111,2496
Non-polymers1,04226
Water70339
1
A: U1 small nuclear ribonucleoprotein A
B: 5'-R(*UP*CP*CP*AP*GP*UP*A)-3'
C: Class I ligase ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,18617
Polymers55,6253
Non-polymers56114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: U1 small nuclear ribonucleoprotein A
E: 5'-R(*UP*CP*CP*AP*GP*UP*A)-3'
F: Class I ligase ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,10615
Polymers55,6253
Non-polymers48112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.6900, 70.0110, 71.8580
Angle α, β, γ (deg.)99.8470, 99.7350, 103.6510
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11340.315 Da / Num. of mol.: 2 / Fragment: RNA binding domain (UNP residues 1-98) / Mutation: Y31H,Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: p11U1ADb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09012
#2: RNA chain 5'-R(*UP*CP*CP*AP*GP*UP*A)-3'


Mass: 2181.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Ligase substrate
#3: RNA chain Class I ligase ribozyme


Mass: 42102.906 Da / Num. of mol.: 2 / Mutation: C47U / Source method: obtained synthetically
Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE FROM LINEARIZED PLASMID P307HU_C47U
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM sodium cacodylate, pH 6.0, 20 mM calcium acetate, 10 mM strontium acetate, 1mM spermine, 16-20% MPD, crystals in same conditions with 30% MPD were crushed and used as microseeding ...Details: 50 mM sodium cacodylate, pH 6.0, 20 mM calcium acetate, 10 mM strontium acetate, 1mM spermine, 16-20% MPD, crystals in same conditions with 30% MPD were crushed and used as microseeding stocks, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. obs: 18190 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.5
Reflection shellResolution: 3.15→3.26 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.1 / % possible all: 94.1

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HHN

3hhn


Resolution: 3.15→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 910 RANDOM
Rwork0.212 --
all-18190 -
obs-17280 -
Displacement parametersBiso mean: 89.83 Å2
Refinement stepCycle: LAST / Resolution: 3.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 5862 26 39 7402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015855
X-RAY DIFFRACTIONf_angle_d1.1331887
X-RAY DIFFRACTIONf_chiral_restr0.04786
X-RAY DIFFRACTIONf_plane_restr0.00397
X-RAY DIFFRACTIONf_dihedral_angle_d19.8691973
X-RAY DIFFRACTIONf_nbd_refined4.0831329
LS refinement shellResolution: 3.1327→3.164 Å / Total num. of bins used: 34
RfactorNum. reflection% reflection
Rwork0.2566 240 -
obs--44 %

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