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- PDB-7qr3: Chimpanzee CPEB3 HDV-like ribozyme -

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Basic information

Entry
Database: PDB / ID: 7qr3
TitleChimpanzee CPEB3 HDV-like ribozyme
Components
  • U1 small nuclear ribonucleoprotein A
  • chimpanzee CPEB3 ribozyme
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)
Pan troglodytes (chimpanzee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 10, 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: U1 small nuclear ribonucleoprotein A
C: chimpanzee CPEB3 ribozyme
D: chimpanzee CPEB3 ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6348
Polymers65,4254
Non-polymers2094
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.254, 135.916, 83.254
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Expression vector pET-mod (others) / References: UniProt: M0R221
#2: RNA chain chimpanzee CPEB3 ribozyme


Mass: 22130.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pan troglodytes (chimpanzee)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 19-24% PEG 3350, 0.2 M sodium formate 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: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.18→67.958 Å / Num. obs: 28178 / % possible obs: 93.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 57.16 Å2 / CC1/2: 1 / Net I/σ(I): 24.9
Reflection shellResolution: 2.18→2.355 Å / Num. unique obs: 1410 / CC1/2: 0.543

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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: 2.18→52.65 Å / SU ML: 0.2866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.3423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2769 1431 5.08 %
Rwork0.2408 26741 -
obs0.2426 28172 78.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.17 Å2
Refinement stepCycle: LAST / Resolution: 2.18→52.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 2924 9 84 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164773
X-RAY DIFFRACTIONf_angle_d0.6337098
X-RAY DIFFRACTIONf_chiral_restr0.0722910
X-RAY DIFFRACTIONf_plane_restr0.0029391
X-RAY DIFFRACTIONf_dihedral_angle_d13.882237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.260.4519160.4489266X-RAY DIFFRACTION7.93
2.26-2.350.4378530.3926970X-RAY DIFFRACTION28.91
2.35-2.460.3678870.32931928X-RAY DIFFRACTION56.3
2.46-2.580.38161810.30232938X-RAY DIFFRACTION88.11
2.58-2.750.33581750.28943388X-RAY DIFFRACTION100
2.75-2.960.35651700.31043420X-RAY DIFFRACTION100
2.96-3.260.32251980.29513386X-RAY DIFFRACTION100
3.26-3.730.28981740.24413419X-RAY DIFFRACTION100
3.73-4.70.22471840.2133449X-RAY DIFFRACTION100
4.7-52.650.24441930.20343577X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: -27.2054052585 Å / Origin y: -32.7996086805 Å / Origin z: -3.71457740533 Å
111213212223313233
T0.322796334537 Å2-0.0292910243835 Å20.0245608253139 Å2-0.393308875029 Å20.0560813899104 Å2--0.30930126041 Å2
L0.68786180636 °20.237359673226 °20.438257733162 °2-0.960319795549 °20.336905312362 °2--0.717140109585 °2
S-0.0901638636445 Å °0.138467838449 Å °-0.0582504468978 Å °0.00157220566509 Å °-0.0515147239699 Å °-0.0807262574323 Å °-0.0175087445914 Å °0.188206820758 Å °-0.00970648084584 Å °
Refinement TLS groupSelection details: all

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