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- PDB-4fhv: Crystal structures of the Cid1 poly (U) polymerase reveal the mec... -

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Basic information

Entry
Database: PDB / ID: 4fhv
TitleCrystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity - MgCTP bound
ComponentsPoly(A) RNA polymerase protein cid1
KeywordsTRANSFERASE / nucleotidyltransferase / poly(U) polymerase
Function / homology
Function and homology information


polyuridylation-dependent decapping of nuclear-transcribed mRNA / negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / cytoplasm / cytosol
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
CYTIDINE-5'-TRIPHOSPHATE / Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLunde, B.M. / Magler, I. / Meinhart, A.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity.
Authors: Lunde, B.M. / Magler, I. / Meinhart, A.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Sep 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4643
Polymers39,9571
Non-polymers5072
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.640, 62.720, 111.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39956.754 Da / Num. of mol.: 1 / Fragment: UNP residues 33-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: cid1, SPAC19D5.03 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)RIL
References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 100 mM CHES, pH 9.5, 5-10% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2011
RadiationMonochromator: double crystal sagitally focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→41.739 Å / Num. all: 22692 / Num. obs: 22623 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Net I/σ(I): 16.9
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 6.9 / % possible all: 99.3

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FH3

4fh3


Resolution: 2.1→41.739 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.155 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23566 1122 5 %RANDOM
Rwork0.19266 ---
obs0.19479 21499 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.833 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--1.4 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 30 158 2810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222758
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.091.993737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2165334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90123.359128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48215494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9321519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212074
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.461.51634
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92122647
X-RAY DIFFRACTIONr_scbond_it1.50931124
X-RAY DIFFRACTIONr_scangle_it2.6224.51084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 75 -
Rwork0.211 1544 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.47940.2013-1.95280.65170.09352.14850.0215-0.0729-0.11880.1372-0.1113-0.00080.0312-0.0540.08980.0381-0.0216-0.00690.0290.00240.0125-16.8453-3.46642.1645
21.31850.2674-0.13820.9496-0.04570.8875-0.00950.029-0.0045-0.007-0.0245-0.0157-0.033-0.03280.0340.03660.0036-0.01230.0366-0.00120.0114-11.54565.3983-17.4801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 152
2X-RAY DIFFRACTION2A153 - 377

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