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- PDB-4e7x: Structural Basis for the Activity of a Cytoplasmic RNA Terminal U... -

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Basic information

Entry
Database: PDB / ID: 4e7x
TitleStructural Basis for the Activity of a Cytoplasmic RNA Terminal U-transferase
ComponentsPoly(A) RNA polymerase protein cid1
KeywordsTRANSFERASE / Beta polymerase-like nucleotidyl transferase / terminal uridine transferase / UTP / RNA / cytoplasmic
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 ...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
ACETATE ION / Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYates, L.A. / Fleurdepine, S. / Rissland, O.S. / DeColibus, L. / Harlos, K. / Norbury, C.J. / Gilbert, R.J.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis for the activity of a cytoplasmic RNA terminal uridylyl transferase.
Authors: Yates, L.A. / Fleurdepine, S. / Rissland, O.S. / De Colibus, L. / Harlos, K. / Norbury, C.J. / Gilbert, R.J.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Aug 22, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Poly(A) RNA polymerase protein cid1
D: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,5158
Polymers185,2794
Non-polymers2364
Water18010
1
A: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3792
Polymers46,3201
Non-polymers591
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)46,3792
Polymers46,3201
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3792
Polymers46,3201
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3792
Polymers46,3201
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.430, 78.000, 151.540
Angle α, β, γ (deg.)90.00, 109.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 46319.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: cid1, SPAC19D5.03 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 15% (v/v) glycerol, 25.5% (w/v) PEG4000, 170mM ammonium acetate, 85mM tri-sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.973 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 3.2→64.27 Å / Num. all: 30013 / Num. obs: 30013 / % possible obs: 99.5 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Biso Wilson estimate: 82.64 Å2 / Rmerge(I) obs: 0.138

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→64.27 Å / Cor.coef. Fo:Fc: 0.9306 / Cor.coef. Fo:Fc free: 0.9075 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1523 5.07 %RANDOM
Rwork0.1788 ---
obs0.1805 30013 --
Displacement parametersBiso mean: 73.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.9441 Å20 Å21.1909 Å2
2---3.0386 Å20 Å2
3---2.0945 Å2
Refine analyzeLuzzati coordinate error obs: 0.569 Å
Refinement stepCycle: LAST / Resolution: 3.2→64.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10262 0 16 10 10288
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910513HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9314181HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4870SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1503HARMONIC5
X-RAY DIFFRACTIONt_it10513HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion3.13
X-RAY DIFFRACTIONt_chiral_improper_torsion1332SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11559SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2926 160 5.57 %
Rwork0.246 2710 -
all0.2487 2870 -
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)
11.48520.21220.04442.96350.72060.8917-0.01390.1103-0.36120.0316-0.08420.1620.1546-0.02450.0981-0.092-0.15260.0354-0.1753-0.0243-0.0362-12.6285-13.521822.1647
20.93060.31860.39682.03030.77631.8696-0.03590.07260.0877-0.00030.1355-0.06740.00820.1789-0.0996-0.1194-0.0094-0.0625-0.13290.0102-0.02715.8501-38.768555.9948
32.7906-0.4043-0.84361.70410.08242.19480.07020.09150.2356-0.02810.0330.0802-0.1215-0.1659-0.1033-0.2489-0.0885-0.0456-0.17660.00750.0044-26.993-49.994443.4287
42.6498-0.6209-0.69521.66360.60742.61860.08590.16810.0117-0.1968-0.053-0.2806-0.18820.085-0.0328-0.1191-0.0683-0.0392-0.16340.0375-0.146821.3954-60.242813.0112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|41 - A|109 A|115 - A|149 A|152 - A|308 A|322 - A|379 }A41 - 109
2X-RAY DIFFRACTION1{ A|41 - A|109 A|115 - A|149 A|152 - A|308 A|322 - A|379 }A115 - 149
3X-RAY DIFFRACTION1{ A|41 - A|109 A|115 - A|149 A|152 - A|308 A|322 - A|379 }A152 - 308
4X-RAY DIFFRACTION1{ A|41 - A|109 A|115 - A|149 A|152 - A|308 A|322 - A|379 }A322 - 379
5X-RAY DIFFRACTION2{ B|41 - B|109 B|115 - B|147 B|158 - B|308 B|322 - B|363 }B41 - 109
6X-RAY DIFFRACTION2{ B|41 - B|109 B|115 - B|147 B|158 - B|308 B|322 - B|363 }B115 - 147
7X-RAY DIFFRACTION2{ B|41 - B|109 B|115 - B|147 B|158 - B|308 B|322 - B|363 }B158 - 308
8X-RAY DIFFRACTION2{ B|41 - B|109 B|115 - B|147 B|158 - B|308 B|322 - B|363 }B322 - 363
9X-RAY DIFFRACTION3{ C|41 - C|109 C|115 - C|147 C|156 - C|311 C|322 - C|379 }C41 - 109
10X-RAY DIFFRACTION3{ C|41 - C|109 C|115 - C|147 C|156 - C|311 C|322 - C|379 }C115 - 147
11X-RAY DIFFRACTION3{ C|41 - C|109 C|115 - C|147 C|156 - C|311 C|322 - C|379 }C156 - 311
12X-RAY DIFFRACTION3{ C|41 - C|109 C|115 - C|147 C|156 - C|311 C|322 - C|379 }C322 - 379
13X-RAY DIFFRACTION4{ D|41 - D|109 D|115 - D|149 D|156 - D|312 D|322 - D|380 }D41 - 109
14X-RAY DIFFRACTION4{ D|41 - D|109 D|115 - D|149 D|156 - D|312 D|322 - D|380 }D115 - 149
15X-RAY DIFFRACTION4{ D|41 - D|109 D|115 - D|149 D|156 - D|312 D|322 - D|380 }D156 - 312
16X-RAY DIFFRACTION4{ D|41 - D|109 D|115 - D|149 D|156 - D|312 D|322 - D|380 }D322 - 380

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