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- PDB-4nku: Structure of Cid1 in complex with its short product ApU -

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Basic information

Entry
Database: PDB / ID: 4nku
TitleStructure of Cid1 in complex with its short product ApU
Components
  • 5'-R(*AP*U)-3'
  • Poly(A) RNA polymerase protein cid1
KeywordsTRANSFERASE/RNA / poly(U) polymerase / nucleotidyl tranfer domain / PAP-associated domain / UTP binding / TRANSFERASE-RNA complex
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)-polymerase, middle domain / Polymerase, nucleotidyl transferase 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)-polymerase, middle domain / Polymerase, nucleotidyl transferase 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
BROMIDE ION / RNA / Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: Poly(A) RNA polymerase protein cid1
B: Poly(A) RNA polymerase protein cid1
D: 5'-R(*AP*U)-3'
H: 5'-R(*AP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46310
Polymers79,1504
Non-polymers3136
Water6,413356
1
A: Poly(A) RNA polymerase protein cid1
D: 5'-R(*AP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7846
Polymers39,5752
Non-polymers2084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-24 kcal/mol
Surface area16230 Å2
MethodPISA
2
B: Poly(A) RNA polymerase protein cid1
H: 5'-R(*AP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6794
Polymers39,5752
Non-polymers1042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-15 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.020, 77.090, 81.830
Angle α, β, γ (deg.)90.00, 90.71, 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: RNA chain 5'-R(*AP*U)-3'


Mass: 590.414 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
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: 1.94→45.337 Å / Num. all: 49786 / Num. obs: 49569 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.14
Reflection shellHighest resolution: 1.94 Å / Redundancy: 5 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 2.28 / % possible all: 99.2

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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: 1.94→45.337 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 2001 4.04 %
Rwork0.1792 --
obs0.181 49569 99.54 %
all-49786 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→45.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 78 6 356 5551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075339
X-RAY DIFFRACTIONf_angle_d1.0777220
X-RAY DIFFRACTIONf_dihedral_angle_d15.3642013
X-RAY DIFFRACTIONf_chiral_restr0.078794
X-RAY DIFFRACTIONf_plane_restr0.006899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.98840.2721340.21753359X-RAY DIFFRACTION99
1.9884-2.04220.23231420.20793396X-RAY DIFFRACTION99
2.0422-2.10230.27991480.19853348X-RAY DIFFRACTION99
2.1023-2.17010.27091470.19633359X-RAY DIFFRACTION100
2.1701-2.24770.27231330.19723422X-RAY DIFFRACTION99
2.2477-2.33770.26051500.18813392X-RAY DIFFRACTION100
2.3377-2.44410.26031480.18543371X-RAY DIFFRACTION100
2.4441-2.57290.25121310.18473424X-RAY DIFFRACTION100
2.5729-2.73410.27471460.19473376X-RAY DIFFRACTION100
2.7341-2.94520.2291560.18993395X-RAY DIFFRACTION100
2.9452-3.24150.22271410.18393418X-RAY DIFFRACTION100
3.2415-3.71030.2041450.16193414X-RAY DIFFRACTION100
3.7103-4.67390.16891400.14943439X-RAY DIFFRACTION100
4.6739-45.34970.21851400.18163455X-RAY DIFFRACTION98

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