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- PDB-1m5v: Transition State Stabilization by a Catalytic RNA -

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Basic information

Entry
Database: PDB / ID: 1m5v
TitleTransition State Stabilization by a Catalytic RNA
Components
  • (RNA INHIBITOR ...) x 2
  • RNA HAIRPIN RIBOZYME
  • U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
KeywordsTRANSLATION/RNA / HAIRPIN RIBOZYME / CATALYTIC RNA / U1A RNA BINDING PROTEIN 2'3'cyclic phosphate / cleaved substrate / TRANSLATION-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) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRupert, P.B. / Massey, A.P. / Sigurdsson, S.T. / Ferre-D'Amare, A.R.
Citation
Journal: Science / Year: 2002
Title: Transition state stabilization by a catalytic RNA
Authors: Rupert, P.B. / Massey, A.P. / Sigurdsson, S.T. / Ferre-D'Amare, A.R.
#1: Journal: Nature / Year: 2001
Title: Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
Authors: Rupert, P.B. / Ferre-D'Amare, A.R.
History
DepositionJul 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA INHIBITOR SUBSTRATE
M: RNA INHIBITOR SUBSTRATE
B: RNA HAIRPIN RIBOZYME
D: RNA INHIBITOR SUBSTRATE
P: RNA INHIBITOR SUBSTRATE
E: RNA HAIRPIN RIBOZYME
C: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,44944
Polymers95,8508
Non-polymers1,59936
Water4,270237
1
A: RNA INHIBITOR SUBSTRATE
M: RNA INHIBITOR SUBSTRATE
B: RNA HAIRPIN RIBOZYME
C: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,56418
Polymers47,9254
Non-polymers63914
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RNA INHIBITOR SUBSTRATE
P: RNA INHIBITOR SUBSTRATE
E: RNA HAIRPIN RIBOZYME
F: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,88526
Polymers47,9254
Non-polymers96022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)258.648, 44.258, 102.174
Angle α, β, γ (deg.)90.00, 107.69, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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RNA INHIBITOR ... , 2 types, 4 molecules ADMP

#1: RNA chain RNA INHIBITOR SUBSTRATE


Mass: 3872.317 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS
#2: RNA chain RNA INHIBITOR SUBSTRATE


Mass: 2744.655 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS

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RNA chain / Protein , 2 types, 4 molecules BECF

#3: RNA chain RNA HAIRPIN RIBOZYME


Mass: 29809.795 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS
#4: Protein U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1 snRNP A protein / U1 snRNP-specific protein A


Mass: 11498.472 Da / Num. of mol.: 2 / Fragment: U1A RNA BINDING DOMAIN / 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

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Non-polymers , 3 types, 273 molecules

#5: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5
Details: MPD, ammonium chloride, calcium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1CaCl211
2NH4Cl11
3MPD11
4CaCl212
5NH4Cl12
6MPD12

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 43840 / Num. obs: 43840 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 37.2 Å2 / Rsym value: 0.06 / Net I/σ(I): 24.7
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 3647 / Rsym value: 0.265 / % possible all: 81.7

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HP6

1hp6
PDB Unreleased entry


Resolution: 2.4→19.7 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4100 9.4 %RANDOM
Rwork0.221 ---
obs0.221 43428 98.9 %-
all-43428 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.407 Å2 / ksol: 0.31455 e/Å3
Displacement parametersBiso mean: 79.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å217.28 Å2
2---3.2 Å20 Å2
3----1.1 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 4818 34 253 6632
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_mcbond_it2.833
X-RAY DIFFRACTIONc_mcangle_it3.584
X-RAY DIFFRACTIONc_scbond_it6.276
X-RAY DIFFRACTIONc_scangle_it7.317
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 459 6.6 %
Rwork0.311 6524 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA_RNA_NEW.
X-RAY DIFFRACTION3DNA-RNA_REPDWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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