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- PDB-2mjh: Solution structure of the GLD-1 RNA-binding domain in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 2mjh
TitleSolution structure of the GLD-1 RNA-binding domain in complex with RNA
Components
  • 5'-CUACUCAUAU-3'
  • Female germline-specific tumor suppressor gld-1
KeywordsRNA BINDING PROTEIN / GLD-1 / KH-QUA2 domain / STAR protein family / RNA regulation / tra-2
Function / homology
Function and homology information


oocyte fate determination / positive regulation of female gonad development / regulation of germ cell proliferation / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of oocyte development / P granule / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / oogenesis / meiotic cell cycle ...oocyte fate determination / positive regulation of female gonad development / regulation of germ cell proliferation / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of oocyte development / P granule / regulation of mRNA splicing, via spliceosome / post-transcriptional regulation of gene expression / oogenesis / meiotic cell cycle / mRNA 3'-UTR binding / mRNA 5'-UTR binding / regulation of gene expression / negative regulation of translation / single-stranded RNA binding / negative regulation of gene expression / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain ...STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / KH domain-containing BBP-like / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Female germline-specific tumor suppressor gld-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model15
AuthorsDaubner, G.M. / Allain, F.H.-T.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1.
Authors: Daubner, G.M. / Brummer, A. / Tocchini, C. / Gerhardy, S. / Ciosk, R. / Zavolan, M. / Allain, F.H.
History
DepositionJan 9, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Female germline-specific tumor suppressor gld-1
B: 5'-CUACUCAUAU-3'


Theoretical massNumber of molelcules
Total (without water)19,1582
Polymers19,1582
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-21 kcal/mol
Surface area10370 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250Lowest energy and NOE violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Female germline-specific tumor suppressor gld-1 / Defective in germ line development protein 1


Mass: 16075.546 Da / Num. of mol.: 1 / Fragment: KH-QUA2 domain of GLD-1, UNP residues 195-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata)
Description: Purification via the IMPACT system (NEB) that results in the protein without any additional residues
Gene: gld-1, T23G11.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q17339
#2: RNA chain 5'-CUACUCAUAU-3'


Mass: 3082.868 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1242D 1H-13C HSQC
1323D HNCA
1423D HN(CO)CA
1523D HNCO
1623D HN(CA)CO
1723D CBCA(CO)NH
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11132D 1H-1H TOCSY
11232D 1H-1H NOESY
11332D F1f F2f 1H-1H NOESY
11412D 1H-13C HSQC
11542D F2f 1H-1H NOESY
11643D F1f F2e 1H-1H NOESY
1171Long-range 1H-15N HSQC
11813D HNHA
11962D 1H-15N IPAP HSQC
12052D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.45 mM [U-15N] GLD-1 (aa 195-336), 0.45 mM 5'-CUACUCAUAU-3', 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.45 mM [U-13C; U-15N] GLD-1 (aa 195-336), 0.45 mM 5'-CUACUCAUAU-3', 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.45 mM [U-15N] GLD-1 (aa 195-336), 0.45 mM 5'-CUACUCAUAU-3', 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM DTT, 100% D2O100% D2O
40.45 mM [U-13C; U-15N] GLD-1 (aa 195-336), 0.45 mM 5'-CUACUCAUAU-3', 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM DTT, 100% D2O100% D2O
50.45 mM [U-10% 13C; U-100% 15N] GLD-1 (aa 195-336), 0.45 mM 5'-CUACUCAUAU-3', 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
60.45 mM [U-15N] GLD-1 (aa 195-336), 0.45 mM 5'-CUACUCAUAU-3', 50 mM sodium chloride, 20 mM sodium phosphate, 3 mM DTT, 14 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.45 mMGLD-1 (aa 195-336)-1[U-15N]1
0.45 mM5'-CUACUCAUAU-3'-21
50 mMsodium chloride-31
20 mMsodium phosphate-41
3 mMDTT-51
0.45 mMGLD-1 (aa 195-336)-6[U-13C; U-15N]2
0.45 mM5'-CUACUCAUAU-3'-72
50 mMsodium chloride-82
20 mMsodium phosphate-92
3 mMDTT-102
0.45 mMGLD-1 (aa 195-336)-11[U-15N]3
0.45 mM5'-CUACUCAUAU-3'-123
50 mMsodium chloride-133
20 mMsodium phosphate-143
3 mMDTT-153
0.45 mMGLD-1 (aa 195-336)-16[U-13C; U-15N]4
0.45 mM5'-CUACUCAUAU-3'-174
50 mMsodium chloride-184
20 mMsodium phosphate-194
3 mMDTT-204
0.45 mMGLD-1 (aa 195-336)-21[U-10% 13C; U-100% 15N]5
0.45 mM5'-CUACUCAUAU-3'-225
50 mMsodium chloride-235
20 mMsodium phosphate-245
3 mMDTT-255
0.45 mMGLD-1 (aa 195-336)-26[U-15N]6
0.45 mM5'-CUACUCAUAU-3'-276
50 mMsodium chloride-286
20 mMsodium phosphate-296
3 mMDTT-306
14 mg/mLPf1 phage-316
Sample conditionsIonic strength: 0.17 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE7504
Bruker AvanceBrukerAVANCE9005

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.114Goddardchemical shift assignment
TopSpin3Bruker Biospincollection
TALOS+Cornilescu, Delaglio and Baxcollection
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
ATNOSCANDID2.1Herrmann, Guntert and Wuthrichpeak picking
PALES2.1Zweckstetter, Hummer and Baxdata analysis
WHAT IF10.1.1Vrienddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: ff99SB force-field/ implicit water
NMR constraintsNOE constraints total: 2899 / NOE intraresidue total count: 669 / NOE long range total count: 609 / NOE medium range total count: 628 / NOE sequential total count: 841
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: Lowest energy and NOE violations
Conformers calculated total number: 250 / Conformers submitted total number: 20

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