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- PDB-2l9b: Heterodimer between Rna14p monkeytail domain and Rna15p hinge dom... -

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Basic information

Entry
Database: PDB / ID: 2l9b
TitleHeterodimer between Rna14p monkeytail domain and Rna15p hinge domain of the yeast CF IA complex
Components
  • mRNA 3'-end-processing protein RNA14
  • mRNA 3'-end-processing protein RNA15
KeywordsTRANSCRIPTION / 3' END MRNA MATURATION
Function / homology
Function and homology information


mRNA cleavage stimulating factor complex / response to DNA damage checkpoint signaling / mRNA cleavage factor complex / RNA 3'-end processing / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA processing / molecular adaptor activity / mRNA binding / mitochondrion ...mRNA cleavage stimulating factor complex / response to DNA damage checkpoint signaling / mRNA cleavage factor complex / RNA 3'-end processing / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA processing / molecular adaptor activity / mRNA binding / mitochondrion / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1660 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #630 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / mRNA 3'-end-processing protein Rna14-like / Transcription termination and cleavage factor C-terminal / Suppressor of forked / Suppressor of forked protein (Suf) / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1660 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #630 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / mRNA 3'-end-processing protein Rna14-like / Transcription termination and cleavage factor C-terminal / Suppressor of forked / Suppressor of forked protein (Suf) / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Special / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
mRNA 3'-end-processing protein RNA14 / mRNA 3'-end-processing protein RNA15
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsMoreno-Morcillo, M. / Minvielle-Sebastia, L. / Fribourg, S. / Mackereth, C.D.
CitationJournal: Structure / Year: 2011
Title: Locked Tether Formation by Cooperative Folding of Rna14p Monkeytail and Rna15p Hinge Domains in the Yeast CF IA Complex.
Authors: Moreno-Morcillo, M. / Minvielle-Sebastia, L. / Fribourg, S. / Mackereth, C.D.
History
DepositionFeb 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 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

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Assembly

Deposited unit
A: mRNA 3'-end-processing protein RNA15
B: mRNA 3'-end-processing protein RNA14


Theoretical massNumber of molelcules
Total (without water)18,1072
Polymers18,1072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein mRNA 3'-end-processing protein RNA15


Mass: 12051.782 Da / Num. of mol.: 1 / Fragment: sequence database residues 127-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: N-terminal His6-tag followed by TEV protease cleavage site. Co-expressed with Rna14p
Gene: RNA15, YGL044C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysY / References: UniProt: P25299
#2: Protein mRNA 3'-end-processing protein RNA14


Mass: 6054.875 Da / Num. of mol.: 1 / Fragment: C-terminal residues 626-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: Co-expressed with Rna14p / Gene: RNA14, YMR061W, YM9796.14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysY / References: UniProt: P25298

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the minimal tether complex between yeast Rna14p and Rna15p
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1333D 1H-13C NOESY aliphatic
1443D 1H-13C NOESY aliphatic
1512D 1H-15N TROSY spin-state selective
1612D 1H-15N TROSY spin-state selective
1773D HNCO
1873D HN(CA)CO
1973D HNCA
11073D HN(CO)CA
11173D HN(CA)CB
11273D CBCA(CO)NH
11373D HNHA
11473D C(CO)NH
11573D H(CCO)NH
11612D 1H-15N HMBC
11712D 1H-15N HSQC
11853D H(CCO)NH
11922D 1H-13C HSQC
12022D HBHD
12122D HBHE
12223D HCACO
12323D (H)CCH-TOCSY
12423D (H)CCH-TOCSY
12583D H(CCO)NH
12632D 1H-13C HSQC
12733D (H)CCH-TOCSY
12833D (H)CCH-TOCSY
12963D HNCO
13043D HCACO
13143D (H)CCH-TOCSY
13243D (H)CCH-TOCSY
13392D 1H-13C HSQC CT
134102D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-1 mM [U-99% 15N] Rna15p, 0.2-1 mM [U-99% 15N] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-99% 13C; U-99% 15N] Rna15p, 0.4 mM [U-99% 13C; U-99% 15N] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 100 % D2O, 100% D2O100% D2O
30.5 mM [U-99% 13C; U-99% 15N; U-99% 2H; 1H I,L,V-methyl] Rna15p, 0.5 mM [U-99% 13C; U-99% 15N; U-99% 2H; 1H I,L,V-methyl] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 100 % D2O, 100% D2O100% D2O
41 mM [U-15N, U-13C]-Leu Rna15p, 1 mM [U-15N, U-13C]-Leu Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 100 % D2O, 100% D2O100% D2O
50.4 mM [U-99% 13C; U-99% 15N] Rna15p, 0.4 mM [U-99% 13C; U-99% 15N] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
61 mM [U-15N, U-13C]-Leu Rna15p, 1 mM [U-15N, U-13C]-Leu Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
71 mM [U-100% 13C; U-100% 15N; U-70% 2H] Rna15p, 1 mM [U-100% 13C; U-100% 15N; U-70% 2H] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
80.5 mM [U-99% 13C; U-99% 15N; U-99% 2H; 1H I,L,V-methyl] Rna15p, 0.5 mM [U-99% 13C; U-99% 15N; U-99% 2H, 1H I,L,V-methyl] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
91 mM [U-10% 13C; U-99% 15N] Rna15p, 1 mM [U-10% 13C; U-99% 15N] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 10 % D2O, 100% D2O100% D2O
100.2 mM [U-99% 15N] Rna15p, 0.2 mM [U-99% 15N] Rna14p, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRna15p-1[U-99% 15N]0.2-11
mMRna14p-2[U-99% 15N]0.2-11
20 mMsodium phosphate-31
50 mMsodium chloride-41
2 mMDTT-51
10 %D2O-61
0.4 mMRna15p-7[U-99% 13C; U-99% 15N]2
0.4 mMRna14p-8[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-92
50 mMsodium chloride-102
2 mMDTT-112
100 %D2O-122
0.5 mMRna15p-13[U-99% 13C; U-99% 15N; U-99% 2H; 1H I,L,V-methyl]3
0.5 mMRna14p-14[U-99% 13C; U-99% 15N; U-99% 2H; 1H I,L,V-methyl]3
20 mMsodium phosphate-153
50 mMsodium chloride-163
2 mMDTT-173
100 %D2O-183
1 mMRna15p-19[U-15N, U-13C]-Leu4
1 mMRna14p-20[U-15N, U-13C]-Leu4
20 mMsodium phosphate-214
50 mMsodium chloride-224
2 mMDTT-234
100 %D2O-244
0.4 mMRna15p-25[U-99% 13C; U-99% 15N]5
0.4 mMRna14p-26[U-99% 13C; U-99% 15N]5
20 mMsodium phosphate-275
50 mMsodium chloride-285
2 mMDTT-295
10 %D2O-305
1 mMRna15p-31[U-15N, U-13C]-Leu6
1 mMRna14p-32[U-15N, U-13C]-Leu6
20 mMsodium phosphate-336
50 mMsodium chloride-346
2 mMDTT-356
10 %D2O-366
1 mMRna15p-37[U-100% 13C; U-100% 15N; U-70% 2H]7
1 mMRna14p-38[U-100% 13C; U-100% 15N; U-70% 2H]7
20 mMsodium phosphate-397
50 mMsodium chloride-407
2 mMDTT-417
10 %D2O-427
0.5 mMRna15p-43[U-99% 13C; U-99% 15N; U-99% 2H; 1H I,L,V-methyl]8
0.5 mMRna14p-44[U-99% 13C; U-99% 15N; U-99% 2H, 1H I,L,V-methyl]8
20 mMsodium phosphate-458
50 mMsodium chloride-468
2 mMDTT-478
10 %D2O-488
1 mMRna15p-49[U-10% 13C; U-99% 15N]9
1 mMRna14p-50[U-10% 13C; U-99% 15N]9
20 mMsodium phosphate-519
50 mMsodium chloride-529
2 mMDTT-539
10 %D2O-549
0.2 mMRna15p-55[U-99% 15N]10
0.2 mMRna14p-56[U-99% 15N]10
20 mMsodium phosphate-5710
50 mMsodium chloride-5810
2 mMDTT-5910
100 %D2O-6010
Sample conditionsIonic strength: 0.07 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA1.2/CNS1.1refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 4168 / NOE intraresidue total count: 1226 / NOE long range total count: 621 / NOE medium range total count: 454 / NOE sequential total count: 604 / Hydrogen bond constraints total count: 100 / Protein chi angle constraints total count: 42 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 114 / Protein psi angle constraints total count: 112
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.5 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å

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