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- PDB-5jnb: structure of GLD-2/RNP-8 complex -

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Basic information

Entry
Database: PDB / ID: 5jnb
Titlestructure of GLD-2/RNP-8 complex
Components
  • Poly(A) RNA polymerase gld-2
  • RNP (RRM RNA binding domain) containing
KeywordsTRANSFERASE / Translational control / Nucleotidyltransferase Poly(A) / Polymerase / RNA binding / C. elegans Germline development
Function / homology
Function and homology information


polynucleotide adenylyltransferase activator activity / cytosolic mRNA polyadenylation / poly(G) binding / RNA-directed RNA polymerase complex / positive regulation of meiosis I / RNA 3'-end processing / embryo development ending in birth or egg hatching / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / P granule ...polynucleotide adenylyltransferase activator activity / cytosolic mRNA polyadenylation / poly(G) binding / RNA-directed RNA polymerase complex / positive regulation of meiosis I / RNA 3'-end processing / embryo development ending in birth or egg hatching / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / P granule / RNA polymerase complex / regulation of alternative mRNA splicing, via spliceosome / nucleus organization / regulation of cell division / positive regulation of mitotic nuclear division / meiotic cell cycle / mRNA processing / single-stranded RNA binding / enzyme binding / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
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 / 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 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Poly(A) RNA polymerase gld-2 / RRM domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.486 Å
AuthorsNakel, K. / Bonneau, F. / Basquin, C. / Eckmann, C.R. / Conti, E.
Funding support Germany, 9items
OrganizationGrant numberCountry
German Research FoundationSFB646 Germany
German Research FoundationSFB1035 Germany
German Research FoundationGRK1721 Germany
German Research FoundationFOR1680 Germany
European CommissionERC Advanced Investigator Grant 294371 Germany
European CommissionMarie Curie ITN RNPnet Germany
German Research FoundationEC369/3-1 Germany
German Research FoundationGRK1591 Germany
German Research FoundationBU2451/1-2 Germany
CitationJournal: Rna / Year: 2016
Title: Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity.
Authors: Nakel, K. / Bonneau, F. / Basquin, C. / Habermann, B. / Eckmann, C.R. / Conti, E.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Data collection
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Poly(A) RNA polymerase gld-2
C: Poly(A) RNA polymerase gld-2
D: Poly(A) RNA polymerase gld-2
E: RNP (RRM RNA binding domain) containing
F: RNP (RRM RNA binding domain) containing
G: RNP (RRM RNA binding domain) containing
H: RNP (RRM RNA binding domain) containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,73223
Polymers188,7418
Non-polymers99115
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24400 Å2
ΔGint-191 kcal/mol
Surface area54810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.347, 86.435, 91.907
Angle α, β, γ (deg.)89.88, 93.13, 90.22
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Poly(A) RNA polymerase gld-2 / Defective in germ line development protein 2


Mass: 38746.105 Da / Num. of mol.: 4 / Fragment: UNP residues 546-923 / Mutation: D668A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-2, ZC308.1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O17087, polynucleotide adenylyltransferase
#2: Protein
RNP (RRM RNA binding domain) containing


Mass: 8439.128 Da / Num. of mol.: 4 / Fragment: UNP residues 177-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: rnp-8, CELE_R119.7, R119.7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O61711

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Non-polymers , 4 types, 145 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 18 % (v/v) PEG MME 550, 50 mM Potassium Nitrate, 60 mM Magnesium Nitrate, 30 mM Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.486→46.26 Å / Num. obs: 135156 / % possible obs: 95.6 % / Redundancy: 2.48 % / CC1/2: 0.993 / Rsym value: 0.088 / Net I/σ(I): 8.8
Reflection shellRsym value: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZRL

4zrl


Resolution: 2.486→46.254 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 6764 5.01 %
Rwork0.1919 --
obs0.1944 135097 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.486→46.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10588 0 58 130 10776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910846
X-RAY DIFFRACTIONf_angle_d1.19414721
X-RAY DIFFRACTIONf_dihedral_angle_d15.8473853
X-RAY DIFFRACTIONf_chiral_restr0.0441686
X-RAY DIFFRACTIONf_plane_restr0.0061888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4856-2.51380.36822140.30674068X-RAY DIFFRACTION90
2.5138-2.54340.33182210.27374226X-RAY DIFFRACTION95
2.5434-2.57440.28052270.24474283X-RAY DIFFRACTION96
2.5744-2.6070.28052260.23414251X-RAY DIFFRACTION96
2.607-2.64130.30742280.24184296X-RAY DIFFRACTION95
2.6413-2.67750.32222200.24314214X-RAY DIFFRACTION95
2.6775-2.71570.27582260.2364301X-RAY DIFFRACTION95
2.7157-2.75620.32442260.23944225X-RAY DIFFRACTION96
2.7562-2.79930.30312300.23544294X-RAY DIFFRACTION95
2.7993-2.84520.30052280.22734332X-RAY DIFFRACTION96
2.8452-2.89420.24872250.22514218X-RAY DIFFRACTION96
2.8942-2.94690.29752250.22254252X-RAY DIFFRACTION96
2.9469-3.00350.27652230.22384335X-RAY DIFFRACTION96
3.0035-3.06480.26412280.22424311X-RAY DIFFRACTION96
3.0648-3.13150.26952290.24298X-RAY DIFFRACTION96
3.1315-3.20430.24762290.20144332X-RAY DIFFRACTION97
3.2043-3.28440.24872290.19974348X-RAY DIFFRACTION97
3.2844-3.37320.24692250.20244292X-RAY DIFFRACTION97
3.3732-3.47240.23062300.20354381X-RAY DIFFRACTION97
3.4724-3.58440.27972300.20244334X-RAY DIFFRACTION97
3.5844-3.71250.22982250.18934320X-RAY DIFFRACTION97
3.7125-3.86110.21082280.18074353X-RAY DIFFRACTION97
3.8611-4.03670.22862230.16984284X-RAY DIFFRACTION96
4.0367-4.24940.19722250.16034290X-RAY DIFFRACTION96
4.2494-4.51540.20232250.15164323X-RAY DIFFRACTION96
4.5154-4.86370.20792210.15844235X-RAY DIFFRACTION95
4.8637-5.35250.25472200.17364200X-RAY DIFFRACTION94
5.3525-6.12550.24832290.19814261X-RAY DIFFRACTION95
6.1255-7.71170.25382250.19564253X-RAY DIFFRACTION95
7.7117-46.26160.19432240.1684223X-RAY DIFFRACTION95

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