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- PDB-4zrl: Structure of the non canonical Poly(A) polymerase complex GLD-2 -... -

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Basic information

Entry
Database: PDB / ID: 4zrl
TitleStructure of the non canonical Poly(A) polymerase complex GLD-2 - GLD-3
Components
  • Defective in germ line development protein 3
  • Poly(A) RNA polymerase gld-2
KeywordsTRANSFERASE / cytoplasmic poly(A)polymerase / post-transcriptional regulation / polyadenylation / non canonical poly(A) polymerase
Function / homology
Function and homology information


germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / : / vulval development / nematode larval development / germ-line stem cell division / RNA-directed RNA polymerase complex / positive regulation of meiosis I / positive regulation of meiotic nuclear division ...germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / : / vulval development / nematode larval development / germ-line stem cell division / RNA-directed RNA polymerase complex / positive regulation of meiosis I / positive regulation of meiotic nuclear division / nuclear division / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / positive regulation of multicellular organism growth / P granule / cytosolic mRNA polyadenylation / embryo development ending in birth or egg hatching / nucleus organization / : / RNA polymerase complex / regulation of cell division / mitotic cytokinesis / positive regulation of mitotic nuclear division / meiotic cell cycle / mRNA processing / regulation of translation / spermatogenesis / protein domain specific binding / positive regulation of gene expression / perinuclear region of cytoplasm / protein-containing complex / RNA binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
GLD-3, KH5 domain / : / : / GLD-3 KH domain 5 / GLD-3, KH3 domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Poly(A) RNA polymerase gld-2 / Defective in germ line development protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsNakel, K. / Bonneau, F. / Eckmann, C.R. / Conti, E.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationBU2451/1-2 Germany
EC | European Research Council (ERC): Elena Conti ERC Advanced Investigator Grant294371
German Research FoundationSFB646, SFB1035, GRK1721, FOR1680
German Research FoundationFOR855, EC369/3-1
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for the activation of the C. elegans noncanonical cytoplasmic poly(A)-polymerase GLD-2 by GLD-3.
Authors: Nakel, K. / Bonneau, F. / Eckmann, C.R. / Conti, E.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Jul 13, 2016Group: Data collection
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(A) RNA polymerase gld-2
B: Defective in germ line development protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9963
Polymers50,9602
Non-polymers351
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-29 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.655, 89.367, 94.666
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 gld-2 / Defective in germ line development protein 2


Mass: 41964.980 Da / Num. of mol.: 1 / Fragment: UNP residues 527-923
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-2, ZC308.1 / Plasmid: pETM30 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLyS
References: UniProt: O17087, polynucleotide adenylyltransferase
#2: Protein Defective in germ line development protein 3 / Germline development defective 3


Mass: 8995.428 Da / Num. of mol.: 1 / Fragment: UNP residues 13-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-3, T07F8.3 / Plasmid: pET21d / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLyS / References: UniProt: Q95ZK7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG MME 550, Potassium nitrate, Magnesium Nitrate, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97975 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97975 Å / Relative weight: 1
ReflectionResolution: 2.28→47.3 Å / Num. all: 284963 / Num. obs: 37155 / % possible obs: 98.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 32.85 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.36
Reflection shellResolution: 2.2831→2.42 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.03 / CC1/2: 0.882 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIXdev_1615refinement
XDSdata reduction
SHELXDEphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.28→47.3 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1848 4.98 %Random selection
Rwork0.187 ---
obs0.1892 37101 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 2.28→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 1 115 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033079
X-RAY DIFFRACTIONf_angle_d0.7534173
X-RAY DIFFRACTIONf_dihedral_angle_d14.3781119
X-RAY DIFFRACTIONf_chiral_restr0.027470
X-RAY DIFFRACTIONf_plane_restr0.004538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2831-2.34480.28961130.25862180X-RAY DIFFRACTION80
2.3448-2.41380.30181470.23782782X-RAY DIFFRACTION100
2.4138-2.49180.28541450.21982736X-RAY DIFFRACTION100
2.4918-2.58080.2391410.21832750X-RAY DIFFRACTION100
2.5808-2.68410.25121480.21232768X-RAY DIFFRACTION100
2.6841-2.80630.34421400.20252749X-RAY DIFFRACTION100
2.8063-2.95420.24261450.20472765X-RAY DIFFRACTION100
2.9542-3.13930.22481450.2042736X-RAY DIFFRACTION100
3.1393-3.38160.24181450.18532774X-RAY DIFFRACTION100
3.3816-3.72180.26291400.17852745X-RAY DIFFRACTION100
3.7218-4.260.18731470.15882773X-RAY DIFFRACTION100
4.26-5.3660.17421520.15412742X-RAY DIFFRACTION100
5.366-47.34320.21481400.1852753X-RAY DIFFRACTION100

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