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- PDB-7qr4: human CPEB3 HDV-like ribozyme -

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Basic information

Entry
Database: PDB / ID: 7qr4
Titlehuman CPEB3 HDV-like ribozyme
Components
  • RNA CPEB3 ribozyme
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA / Ribozyme HDV-like CPEB3 intron brain
Function / homology
Function and homology information


RNA-binding region-containing protein RBM41/RNPC3 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / 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
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: 2.83 Å
AuthorsPrzytula-Mally, A.I. / Engilberge, S. / Johannsen, S. / Olieric, V. / Masquida, B. / Sigel, R.K.O.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
University of ZurichFK-18-097 Switzerland
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002 Switzerland
Agence Nationale de la Recherche (ANR)ANR-17-EUR-0023 Switzerland
CitationJournal: Biorxiv / Year: 2022
Title: Anticodon-like loop-mediated dimerization in the crystal structures of HdV-like CPEB3 ribozymes
Authors: Przytula-Mally, A.I. / Engilberge, S. / Johannsen, S. / Olieric, V. / Masquida, B. / Sigel, R.K.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: U1 small nuclear ribonucleoprotein A
B: RNA CPEB3 ribozyme


Theoretical massNumber of molelcules
Total (without water)32,6972
Polymers32,6972
Non-polymers00
Water543
1
A: U1 small nuclear ribonucleoprotein A
B: RNA CPEB3 ribozyme

A: U1 small nuclear ribonucleoprotein A
B: RNA CPEB3 ribozyme


Theoretical massNumber of molelcules
Total (without water)65,3934
Polymers65,3934
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5480 Å2
ΔGint-36 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.451, 131.879, 90.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein U1 small nuclear ribonucleoprotein A


Mass: 10582.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: p11U1ADb / Production host: Expression vector pET-mod (others) / References: UniProt: M0R221
#2: RNA chain RNA CPEB3 ribozyme


Mass: 22114.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 21540012
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 20-24% PEG 3350, 0.2 M sodium citrate tribasic dihydrate and 30-200 mM HEPES-KOH pH 7.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.825→68.055 Å / Num. obs: 6828 / % possible obs: 92.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 93.31 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.7
Reflection shellResolution: 2.825→3.124 Å / Num. unique obs: 342 / CC1/2: 0.574

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1drz

1drz


Resolution: 2.83→65.94 Å / SU ML: 0.389 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.1353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2676 348 5.1 %
Rwork0.2197 6478 -
obs0.2223 6826 58.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.87 Å2
Refinement stepCycle: LAST / Resolution: 2.83→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 1461 0 3 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262371
X-RAY DIFFRACTIONf_angle_d0.61493532
X-RAY DIFFRACTIONf_chiral_restr0.0341455
X-RAY DIFFRACTIONf_plane_restr0.0032195
X-RAY DIFFRACTIONf_dihedral_angle_d17.25021106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-3.560.4012610.27341317X-RAY DIFFRACTION23.94
3.56-9.6140.25882870.21525161X-RAY DIFFRACTION91.29
Refinement TLS params.Method: refined / Origin x: 0.0485657081387 Å / Origin y: 3.17551941062 Å / Origin z: 8.32629500816 Å
111213212223313233
T0.694268269529 Å20.060605311754 Å2-0.00790720804937 Å2-0.864248460315 Å2-0.14523030782 Å2--0.564832036867 Å2
L2.40019114366 °2-0.796830596738 °2-0.0916690145379 °2-2.50640321098 °2-0.587565866797 °2--1.55670269098 °2
S-0.182793396051 Å °-0.18248801716 Å °0.357539855676 Å °0.295871334218 Å °-0.198449298235 Å °0.0599158322084 Å °-0.458364855507 Å °-0.0161680035668 Å °0.363607992661 Å °
Refinement TLS groupSelection details: all

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