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- PDB-4ud4: Structural Plasticity of Cid1 Provides a Basis for its RNA Termin... -

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Basic information

Entry
Database: PDB / ID: 4ud4
TitleStructural Plasticity of Cid1 Provides a Basis for its RNA Terminal Uridylyl Transferase Activity
ComponentsPOLY(A) RNA POLYMERASE PROTEIN CID1
KeywordsTRANSFERASE / URIDYLYLTRANSFERASE ENZYME
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 / cytoplasm / cytosol
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
Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsYates, L.A. / Durrant, B.P. / Fleurdepine, S. / Harlos, K. / Norbury, C.J. / Gilbert, R.J.C.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural plasticity of Cid1 provides a basis for its distributive RNA terminal uridylyl transferase activity.
Authors: Yates, L.A. / Durrant, B.P. / Fleurdepine, S. / Harlos, K. / Norbury, C.J. / Gilbert, R.J.
History
DepositionDec 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5114
Polymers83,3272
Non-polymers1842
Water6,593366
1
A: POLY(A) RNA POLYMERASE PROTEIN CID1


Theoretical massNumber of molelcules
Total (without water)41,6631
Polymers41,6631
Non-polymers00
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)41,8483
Polymers41,6631
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.960, 62.290, 65.500
Angle α, β, γ (deg.)76.34, 81.08, 63.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein POLY(A) RNA POLYMERASE PROTEIN CID1 / CAFFEINE-INDUCED DEATH PROTEIN 1 / CAFFEINE-INDUCED DEATH SUPPRESSOR 1 URIDYLYLTRANSFERASE


Mass: 41663.445 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Plasmid: PGEX-6P-TCID1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7 / Details: 20MM HEPES, 200MM NACL, 0.5MM TCEP, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→45.9 Å / Num. obs: 79749 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 17
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E7X

4e7x


Resolution: 1.74→45.903 Å / SU ML: 0.2 / σ(F): 1.96 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 3999 5 %
Rwork0.1721 --
obs0.1736 79738 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→45.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5171 0 12 366 5549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095320
X-RAY DIFFRACTIONf_angle_d1.0657187
X-RAY DIFFRACTIONf_dihedral_angle_d13.7081984
X-RAY DIFFRACTIONf_chiral_restr0.051785
X-RAY DIFFRACTIONf_plane_restr0.006913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.76050.33941340.28032611X-RAY DIFFRACTION95
1.7605-1.7820.3731410.26972616X-RAY DIFFRACTION96
1.782-1.80450.29031180.25252553X-RAY DIFFRACTION96
1.8045-1.82830.27521400.2462642X-RAY DIFFRACTION96
1.8283-1.85330.25541500.23832586X-RAY DIFFRACTION96
1.8533-1.87980.27321430.22782625X-RAY DIFFRACTION97
1.8798-1.90780.26191420.22892555X-RAY DIFFRACTION96
1.9078-1.93770.27831370.22242626X-RAY DIFFRACTION96
1.9377-1.96940.23891330.20152635X-RAY DIFFRACTION97
1.9694-2.00340.22381240.20012608X-RAY DIFFRACTION97
2.0034-2.03980.24491410.19392648X-RAY DIFFRACTION97
2.0398-2.0790.22821430.18852609X-RAY DIFFRACTION96
2.079-2.12150.22611420.18052591X-RAY DIFFRACTION97
2.1215-2.16760.20961260.18052638X-RAY DIFFRACTION97
2.1676-2.2180.22141440.18082646X-RAY DIFFRACTION97
2.218-2.27350.22511370.17262651X-RAY DIFFRACTION97
2.2735-2.3350.21881320.17322653X-RAY DIFFRACTION97
2.335-2.40370.21341390.17842630X-RAY DIFFRACTION97
2.4037-2.48130.22781460.18852629X-RAY DIFFRACTION97
2.4813-2.56990.22371300.18062682X-RAY DIFFRACTION97
2.5699-2.67280.20841270.18242614X-RAY DIFFRACTION97
2.6728-2.79440.21321470.17932685X-RAY DIFFRACTION98
2.7944-2.94180.21781350.17912625X-RAY DIFFRACTION97
2.9418-3.1260.22451540.18422613X-RAY DIFFRACTION97
3.126-3.36730.20921300.18222568X-RAY DIFFRACTION95
3.3673-3.70610.18381280.16242589X-RAY DIFFRACTION95
3.7061-4.2420.1551510.14232570X-RAY DIFFRACTION95
4.242-5.34320.16471470.14442552X-RAY DIFFRACTION94
5.3432-45.9190.19351380.15422489X-RAY DIFFRACTION92
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)
18.85813.0140.48943.3181-0.3942.4247-0.02350.0246-0.6924-0.3643-0.2982-0.6720.18840.56170.26990.37010.09260.08650.33150.09670.345228.1528-13.9299-28.0141
24.9525-1.152-1.99571.67780.53267.88780.2264-0.49180.02970.2340.1189-0.1216-0.61380.4777-0.21150.4158-0.0857-0.01560.6220.15770.417842.6292.3885-32.0445
32.78770.2274-0.31110.8918-0.16651.76350.07870.2119-0.0036-0.2963-0.1237-0.2044-0.11160.21310.10840.37590.02920.04260.27580.02020.271420.659-5.1089-27.6321
43.15810.7134-0.31083.37720.0172.84270.1762-0.38330.16980.157-0.0965-0.0339-0.33230.0339-0.060.27150.01330.04860.2806-0.05280.195511.5949-0.3943-15.9239
51.7445-0.321-0.86412.3148-1.12981.73510.08030.56270.4664-0.6689-0.00410.0068-0.5733-0.0414-0.03840.48910.10410.06760.33260.03220.328711.14815.2033-30.7536
60.7788-1.59321.12385.8336-1.40741.9556-0.18620.9329-0.3465-0.9948-0.01910.57840.288-0.45560.20870.61390.0028-0.13090.5687-0.10750.48552.1265-15.6986-38.4075
76.2157-0.9073.58952.5187-1.45535.792-0.0079-0.35020.4020.3966-0.2207-0.2439-0.59920.27440.27940.3568-0.07740.01320.30180.02310.258849.768533.63156.8732
84.9594-1.0647-1.04053.989-1.146.47030.057-0.5155-0.22990.349-0.3239-0.4139-0.28440.77180.19030.3356-0.0953-0.07810.54130.14460.390257.84421.864417.5469
92.26340.1935-0.99361.4606-0.38692.5084-0.0443-0.0178-0.2085-0.0853-0.0891-0.19510.06930.13960.12040.17650.00460.00590.19730.0160.256850.685821.3552-6.5043
103.3052-0.5236-0.65133.5898-0.95692.5572-0.1151-0.2137-0.53560.12790.02770.26810.2517-0.17310.07040.3016-0.03860.03310.2980.00950.323240.05815.3020.438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 40 THROUGH 101 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 102 THROUGH 147 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 148 THROUGH 224 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 225 THROUGH 304 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 305 THROUGH 361 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 362 THROUGH 379 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 41 THROUGH 101 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 102 THROUGH 158 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 159 THROUGH 304 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 305 THROUGH 380 )

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