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- PDB-1m5k: Crystal structure of a hairpin ribozyme in the catalytically-acti... -

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Basic information

Entry
Database: PDB / ID: 1m5k
TitleCrystal structure of a hairpin ribozyme in the catalytically-active conformation
Components
  • PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)
  • RNA HAIRPIN RIBOZYME
  • RNA INHIBITOR SUBSTRATE
KeywordsTRANSLATION/RNA / HAIRPIN RIBOZYME / CATALYTIC RNA / U1A RNA BINDING PROTEIN DOCKED CONFORMATION / SUBSTRATE INHIBITOR STRAND / 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 / MAD / Resolution: 2.4 Å
AuthorsRupert, P.B. / 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
SupersessionAug 2, 2002ID: 1HP6
Revision 1.0Aug 2, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 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.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
Revision 1.4Feb 14, 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: RNA INHIBITOR SUBSTRATE
B: RNA HAIRPIN RIBOZYME
D: RNA INHIBITOR SUBSTRATE
E: RNA HAIRPIN RIBOZYME
C: PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)
F: PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,81041
Polymers96,4166
Non-polymers1,39335
Water1,856103
1
D: RNA INHIBITOR SUBSTRATE
E: RNA HAIRPIN RIBOZYME
F: PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,92021
Polymers48,2083
Non-polymers71218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-151 kcal/mol
Surface area23090 Å2
MethodPISA
2
A: RNA INHIBITOR SUBSTRATE
B: RNA HAIRPIN RIBOZYME
C: PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,88920
Polymers48,2083
Non-polymers68117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-123 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.300, 44.100, 102.400
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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RNA chain , 2 types, 4 molecules ADBE

#1: RNA chain RNA INHIBITOR SUBSTRATE


Mass: 6739.887 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS
#2: RNA chain RNA HAIRPIN RIBOZYME


Mass: 29969.754 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS

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Protein , 1 types, 2 molecules CF

#3: Protein 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, 138 molecules

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


Mass: 40.078 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
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, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1CaCl211
2NH4Cl11
3MPD11
4CaCl212
5NH4Cl12
6MPD12
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion / Details: Rupert, P.B., (2001) Nature, 410, 780.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mM1dropMgCl2
220 mM1reservoirCaCl2
32 mM1reservoirNH4VO3
4150-190 mM1reservoirNH4Cl
521 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→61.07 Å / Num. all: 41156 / Num. obs: 41156 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 43.2 Å2 / Rsym value: 0.067 / Net I/σ(I): 22.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3147 / % possible all: 73.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 100 Å / Num. obs: 41290 / % possible obs: 95.6 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 73.9 % / Rmerge(I) obs: 0.261

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→61.07 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1376780.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh & Huber, Parkinson et al.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 4142 10.1 %RANDOM
Rwork0.229 ---
obs0.23 41156 95.2 %-
all-41156 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.68 Å2 / ksol: 0.275 e/Å3
Displacement parametersBiso mean: 86.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å221.97 Å2
2--3.17 Å20 Å2
3----2.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→61.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 4838 35 103 6474
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_mcbond_it5.043.5
X-RAY DIFFRACTIONc_mcangle_it6.214.5
X-RAY DIFFRACTIONc_scbond_it96
X-RAY DIFFRACTIONc_scangle_it10.567
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 527 9.7 %
Rwork0.376 4927 -
obs--76.6 %
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
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.41 / Rfactor Rwork: 0.376

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