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- PDB-4nkt: Structure of Cid1 in complex with the UTP analog UMPNPP -

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Basic information

Entry
Database: PDB / ID: 4nkt
TitleStructure of Cid1 in complex with the UTP analog UMPNPP
ComponentsPoly(A) RNA polymerase protein cid1
KeywordsTRANSFERASE / poly(U) polymerase / nucleotidyl tranfer domain / PAP-associated domain / UTP binding
Function / homology
Function and homology information


polyuridylation-dependent decapping of nuclear-transcribed mRNA / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / magnesium ion binding / RNA binding / ATP binding ...polyuridylation-dependent decapping of nuclear-transcribed mRNA / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / magnesium ion binding / RNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Poly(a)-polymerase, middle domain - #10 / PAP/25A-associated / Cid1 family poly A polymerase / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich ...Poly(a)-polymerase, middle domain - #10 / PAP/25A-associated / Cid1 family poly A polymerase / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2KH / BROMIDE ION / Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMunoz-Tello, P. / Gabus, C. / Thore, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure.
Authors: Munoz-Tello, P. / Gabus, C. / Thore, S.
History
DepositionNov 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...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 / 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_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

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Assembly

Deposited unit
A: Poly(A) RNA polymerase protein cid1
B: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,27311
Polymers77,9692
Non-polymers1,3039
Water9,206511
1
A: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6525
Polymers38,9851
Non-polymers6674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6216
Polymers38,9851
Non-polymers6365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.770, 77.320, 82.110
Angle α, β, γ (deg.)90.00, 90.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(A) RNA polymerase protein cid1 / Caffeine-induced death protein 1


Mass: 38984.703 Da / Num. of mol.: 2 / Fragment: UNP residues 40-377 / Mutation: D160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cid1, SPAC19D5.03 / Plasmid: pET42-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star
References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1 M imidazole/MES, pH 6.1, 20% glycerol, 10% PEG4000, 126 mM halogens (sodium iodide, sodium bromide, sodium fluoride), 10 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2012
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 53096 / Num. obs: 52778 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.41
Reflection shellHighest resolution: 1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.044 / Mean I/σ(I) obs: 11.19 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EP7

4ep7


Resolution: 1.9→19.838 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 1091 2.07 %
Rwork0.1794 --
obs0.1801 52778 99.4 %
all-53096 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 0 65 511 5665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085297
X-RAY DIFFRACTIONf_angle_d1.0827162
X-RAY DIFFRACTIONf_dihedral_angle_d14.8981999
X-RAY DIFFRACTIONf_chiral_restr0.077785
X-RAY DIFFRACTIONf_plane_restr0.004892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.98640.23371330.19556480X-RAY DIFFRACTION100
1.9864-2.0910.25571480.18796444X-RAY DIFFRACTION100
2.091-2.22190.21051350.18616443X-RAY DIFFRACTION100
2.2219-2.39320.22641300.18316443X-RAY DIFFRACTION100
2.3932-2.63350.25961360.18516495X-RAY DIFFRACTION100
2.6335-3.01350.23071370.19336484X-RAY DIFFRACTION100
3.0135-3.79230.19351420.17146510X-RAY DIFFRACTION100
3.7923-19.83920.18191300.16776388X-RAY DIFFRACTION97

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