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- PDB-4e80: Structural Basis for the Activity of a Cytoplasmic RNA Terminal U... -

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Basic information

Entry
Database: PDB / ID: 4.0E+80
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
URIDINE 5'-TRIPHOSPHATE / Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 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)187,2168
Polymers185,2794
Non-polymers1,9374
Water30617
1
A: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8042
Polymers46,3201
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8042
Polymers46,3201
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8042
Polymers46,3201
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8042
Polymers46,3201
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.690, 77.960, 151.680
Angle α, β, γ (deg.)90.00, 109.29, 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-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
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: 3.02→77.72 Å / Num. all: 35591 / Num. obs: 35591 / % possible obs: 99.5 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 3.2 / Biso Wilson estimate: 73.06 Å2

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→28.72 Å / Cor.coef. Fo:Fc: 0.9343 / Cor.coef. Fo:Fc free: 0.9141 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 1783 5.01 %RANDOM
Rwork0.1764 ---
obs0.1777 35591 99.1 %-
Displacement parametersBiso mean: 61.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.0309 Å20 Å20.0278 Å2
2--1.5998 Å20 Å2
3----5.6307 Å2
Refine analyzeLuzzati coordinate error obs: 0.523 Å
Refinement stepCycle: LAST / Resolution: 3.02→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10339 0 116 17 10472
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910699HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9814467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4908SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes235HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1591HARMONIC5
X-RAY DIFFRACTIONt_it10699HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion3.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1363SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11755SEMIHARMONIC4
LS refinement shellResolution: 3.02→3.11 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2712 157 5.47 %
Rwork0.231 2711 -
all0.2332 2868 -
obs--99.1 %
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)
11.27160.2070.16043.23650.51421.5137-0.00040.0942-0.30730.0938-0.0940.22750.3138-0.15640.0944-0.1196-0.1910.0664-0.11-0.0882-0.1148-12.41-13.469522.5766
20.67770.23970.4831.89730.68331.5344-0.01610.0975-0.00070.05660.1206-0.07630.0760.1525-0.1045-0.042-0.0132-0.0376-0.11130.0093-0.061215.9329-39.46156.3986
32.5889-0.3436-0.52881.50210.2451.71130.02980.170.069-0.01330.0260.1549-0.199-0.1524-0.0558-0.1385-0.08480.0072-0.1160.0264-0.1104-27.3214-50.820144.325
42.8067-1.2765-0.94772.13830.90612.67840.1770.21920.0375-0.2709-0.0259-0.2689-0.32590.2495-0.1511-0.1295-0.1072-0.0204-0.12350.0193-0.20421.5792-60.638513.4455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|41 - A|379 A|501 - A|501 }A41 - 379
2X-RAY DIFFRACTION1{ A|41 - A|379 A|501 - A|501 }A501
3X-RAY DIFFRACTION2{ B|41 - B|379 B|501 - B|501 }B41 - 379
4X-RAY DIFFRACTION2{ B|41 - B|379 B|501 - B|501 }B501
5X-RAY DIFFRACTION3{ C|42 - C|381 C|501 - C|501 }C42 - 381
6X-RAY DIFFRACTION3{ C|42 - C|381 C|501 - C|501 }C501
7X-RAY DIFFRACTION4{ D|41 - D|380 D|500 - D|500 }D41 - 380
8X-RAY DIFFRACTION4{ D|41 - D|380 D|500 - D|500 }D500

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