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- PDB-4ep7: Functional implications from the Cid1 poly(U) polymerase crystal ... -

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Basic information

Entry
Database: PDB / ID: 4ep7
TitleFunctional implications from the Cid1 poly(U) polymerase crystal structure
ComponentsPoly(A) RNA polymerase protein cid1
KeywordsTRANSFERASE / poly(U) polymerase / UTP binding
Function / homology
Function and homology information


polyuridylation-dependent decapping of nuclear-transcribed mRNA / : / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / magnesium ion binding / RNA binding ...polyuridylation-dependent decapping of nuclear-transcribed mRNA / : / RNA uridylyltransferase / RNA 3'-end processing / 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 ...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
URIDINE 5'-TRIPHOSPHATE / Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2805 Å
AuthorsMunoz-Tello, P. / Gabus, C. / Thore, S.
CitationJournal: Structure / Year: 2012
Title: Functional implications from the cid1 poly(u) polymerase crystal structure.
Authors: Munoz-Tello, P. / Gabus, C. / Thore, S.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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)79,08211
Polymers77,9432
Non-polymers1,1389
Water4,396244
1
A: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5536
Polymers38,9721
Non-polymers5815
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)39,5295
Polymers38,9721
Non-polymers5574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.490, 76.860, 81.860
Angle α, β, γ (deg.)90.00, 91.17, 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: 38971.660 Da / Num. of mol.: 2 / Fragment: UNP Residues 40-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: cid1, SPAC19D5.03 / Production host: Escherichia coli (E. coli)
References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1M Imidatole/MES pH 6.1, 20% Glycerol, 10% PEG 4000, 42mM NaI, 42mM NaBr, 42mM NaF., 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: 0.9811 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2011
RadiationMonochromator: Channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9811 Å / Relative weight: 1
ReflectionResolution: 2.27→45.193 Å / Num. obs: 29999 / % possible obs: 97.4 % / Observed criterion σ(F): 2.64 / Observed criterion σ(I): 2.64 / Redundancy: 2.79 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.27-2.32.64711159.3
2.3-2.43.933501199.2
2.4-2.54.642942199.2
2.5-37.549607199.3
3-415.887653199.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2805→45.193 Å / SU ML: 0.34 / σ(F): 1.99 / Phase error: 24.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1500 5 %RANDOM
Rwork0.1877 ---
obs0.1907 29996 98.74 %-
all-29996 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.058 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.926 Å2-0 Å22.7324 Å2
2---8.3656 Å20 Å2
3---2.4396 Å2
Refinement stepCycle: LAST / Resolution: 2.2805→45.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5146 0 65 244 5455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115459
X-RAY DIFFRACTIONf_angle_d1.1127188
X-RAY DIFFRACTIONf_dihedral_angle_d17.8322049
X-RAY DIFFRACTIONf_chiral_restr0.071778
X-RAY DIFFRACTIONf_plane_restr0.004898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2805-2.35410.28641330.2032540X-RAY DIFFRACTION97
2.3541-2.43830.2881370.19312587X-RAY DIFFRACTION99
2.4383-2.53590.25421360.192589X-RAY DIFFRACTION100
2.5359-2.65130.25161360.18342588X-RAY DIFFRACTION99
2.6513-2.79110.25911360.18252589X-RAY DIFFRACTION99
2.7911-2.96590.29511370.18912604X-RAY DIFFRACTION99
2.9659-3.19480.24011370.18222599X-RAY DIFFRACTION99
3.1948-3.51620.26651360.17412592X-RAY DIFFRACTION99
3.5162-4.02480.19361380.16682605X-RAY DIFFRACTION99
4.0248-5.06970.20691360.16092590X-RAY DIFFRACTION98
5.0697-45.20210.24681380.20972613X-RAY DIFFRACTION97

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