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- PDB-3r1l: Crystal structure of the Class I ligase ribozyme-substrate prelig... -

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Basic information

Entry
Database: PDB / ID: 3r1l
TitleCrystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Mg2+ 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: 3.125 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 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)112,36752
Polymers111,2496
Non-polymers1,11846
Water91951
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)56,23228
Polymers55,6253
Non-polymers60825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-201 kcal/mol
Surface area26800 Å2
MethodPISA
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)56,13524
Polymers55,6253
Non-polymers51021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-181 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.190, 70.237, 71.214
Angle α, β, γ (deg.)99.860, 99.340, 103.810
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM sodium cacodylate, pH 6.0, 20 mM calcium chloride, 10 mM strontium chloride, 1 mM spermine, 26% MPD, crystals were crushed and used as microseeding stocks, calcium chloride was ...Details: 50 mM sodium cacodylate, pH 6.0, 20 mM calcium chloride, 10 mM strontium chloride, 1 mM spermine, 26% MPD, crystals were crushed and used as microseeding stocks, calcium chloride was replaced with magnesium chloride prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / 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: 3.125→40 Å / Num. obs: 18739 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.135 / Χ2: 1.194 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.15-3.25.40.4699180.467198.1
3.2-3.2660.3899400.509198.4
3.26-3.336.40.3749370.576198.7
3.33-3.396.70.3859360.578198.9
3.39-3.476.90.3699110.586198.9
3.47-3.557.30.349640.654199.2
3.55-3.647.50.3019190.66198.8
3.64-3.737.60.2469540.745199
3.73-3.847.60.2299130.844199.1
3.84-3.977.50.2029660.929199.2
3.97-4.117.60.1869031.028199.2
4.11-4.277.60.1779551.161199.3
4.27-4.477.60.1569501.249199.4
4.47-4.77.60.1419241.389199.4
4.7-57.50.1359391.53199.5
5-5.387.60.1329571.818199.6
5.38-5.927.50.1229322.083199.6
5.92-6.787.40.1179372.114199.8
6.78-8.527.30.0979462.236199.8
8.52-407.30.0749382.126199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HHN

3hhn


Resolution: 3.125→37.9073 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8006 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 964 5.15 %RANDOM
Rwork0.1974 ---
obs-18730 98.67 %-
Solvent computationBsol: 11.869 Å2 / ksol: 0.209 e/Å3
Displacement parametersBiso max: 171.46 Å2 / Biso mean: 76.199 Å2 / Biso min: 34.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.294 Å2-3.251 Å27.469 Å2
2---0.062 Å2-0.719 Å2
3---1.356 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 3.125→37.9073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 5862 46 51 7434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007662
X-RAY DIFFRACTIONf_angle_d1.3272668
X-RAY DIFFRACTIONf_chiral_restr0.055118
X-RAY DIFFRACTIONf_plane_restr0.00381
X-RAY DIFFRACTIONf_dihedral_angle_d20.1972102
X-RAY DIFFRACTIONf_nbd_refined4.0861414
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
3.1249-3.15440.255407X-RAY DIFFRACTION3677
3.1544-3.1850.2609481X-RAY DIFFRACTION3692
3.185-3.21680.2316501X-RAY DIFFRACTION3695
3.2168-3.250.2346491X-RAY DIFFRACTION3694
3.25-3.28450.2253501X-RAY DIFFRACTION3693
3.2845-3.32060.2241488X-RAY DIFFRACTION3696
3.3206-3.35830.2545513X-RAY DIFFRACTION3693
3.3583-3.39780.2355498X-RAY DIFFRACTION3694
3.3978-3.43920.2331464X-RAY DIFFRACTION3694
3.4392-3.48270.2091531X-RAY DIFFRACTION3693
3.4827-3.52850.2126482X-RAY DIFFRACTION3694
3.5285-3.57680.2228472X-RAY DIFFRACTION3695
3.5768-3.62790.211503X-RAY DIFFRACTION3694
3.6279-3.6820.1958520X-RAY DIFFRACTION3693
3.682-3.73950.1874467X-RAY DIFFRACTION3694
3.7395-3.80070.1912500X-RAY DIFFRACTION3694
3.8007-3.86620.1809489X-RAY DIFFRACTION3693
3.8662-3.93640.1891502X-RAY DIFFRACTION3694
3.9364-4.01210.1649498X-RAY DIFFRACTION3694
4.0121-4.09390.1702483X-RAY DIFFRACTION3694
4.0939-4.18280.1803505X-RAY DIFFRACTION3693
4.1828-4.280.1844481X-RAY DIFFRACTION3695
4.28-4.38680.1636507X-RAY DIFFRACTION3695
4.3868-4.50530.1748501X-RAY DIFFRACTION3694
4.5053-4.63760.1801489X-RAY DIFFRACTION3693
4.6376-4.7870.18499X-RAY DIFFRACTION3695
4.787-4.95780.2095499X-RAY DIFFRACTION3695
4.9578-5.15580.198482X-RAY DIFFRACTION3694
5.1558-5.38980.1928528X-RAY DIFFRACTION3694
5.3898-5.67310.1783487X-RAY DIFFRACTION3695
5.6731-6.02720.1905501X-RAY DIFFRACTION3694
6.0272-6.49050.2094497X-RAY DIFFRACTION3695
6.4905-7.13970.2095510X-RAY DIFFRACTION3696
7.1397-8.16380.1947497X-RAY DIFFRACTION3696
8.1638-10.25180.2003508X-RAY DIFFRACTION3695
10.2518-37.91010.1872484X-RAY DIFFRACTION3693

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