BMRB Entry 16425

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16425
MolProbity Validation Chart

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Title:
Interdomain RRM packing contributes to RNA recognition in the rna15, hrp1, anchor RNA 3' processing ternary complex
Deposition date:
2009-07-24
Original release date:
2010-07-27
Authors:
Leeper, Thomas; Varani, Gabriele
Citation:

Citation: Leeper, Thomas; Qu, Xiangping; Lu, Connie; Moore, Claire; Varani, Gabriele. "Novel Protein-Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1."  J. Mol. Biol. 401, 334-349 (2010).
PubMed: 20600122

Assembly members:

Assembly members:
rna15p, polymer, 84 residues, Formula weight is not available
anchor_RNA, polymer, 13 residues, 112.088 Da.
hrp1p, polymer, 167 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pet32

Entity Sequences (FASTA):

Entity Sequences (FASTA):
rna15p: NPPSRVVYLGSIPYDQTEEQ ILDLCSNVGPVINLKMMFDP QTGRSKGYAFIEFRDLESSA SAVRNLNGYQLGSRFLKCGY SSNS
anchor_RNA: UAUAUAUAAUAAU
hrp1p: KESCKMFIGGLNWDTTEDNL REYFGKYGTVTDLKIMKDPA TGRSRGFGFLSFEKPSSVDE VVKTQHILDGKVIDPKRAIP RDEQDKTGKIFVGGIGPDVR PKEFEEFFSQWGTIIDAQLM LDKDTGQSRGFGFVTYDSAD AVDRVCQNKFIDFKDRKIEI KRAEPRH

Data sets:
Data typeCount
13C chemical shifts280
15N chemical shifts88
1H chemical shifts554

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1rna15p1
2anchor_RNA2
3hrp1p3

Entities:

Entity 1, rna15p 84 residues - Formula weight is not available

1   ASNPROPROSERARGVALVALTYRLEUGLY
2   SERILEPROTYRASPGLNTHRGLUGLUGLN
3   ILELEUASPLEUCYSSERASNVALGLYPRO
4   VALILEASNLEULYSMETMETPHEASPPRO
5   GLNTHRGLYARGSERLYSGLYTYRALAPHE
6   ILEGLUPHEARGASPLEUGLUSERSERALA
7   SERALAVALARGASNLEUASNGLYTYRGLN
8   LEUGLYSERARGPHELEULYSCYSGLYTYR
9   SERSERASNSER

Entity 2, anchor_RNA 13 residues - 112.088 Da.

1   UAUAUAUAAU
2   AAU

Entity 3, hrp1p 167 residues - Formula weight is not available

1   LYSGLUSERCYSLYSMETPHEILEGLYGLY
2   LEUASNTRPASPTHRTHRGLUASPASNLEU
3   ARGGLUTYRPHEGLYLYSTYRGLYTHRVAL
4   THRASPLEULYSILEMETLYSASPPROALA
5   THRGLYARGSERARGGLYPHEGLYPHELEU
6   SERPHEGLULYSPROSERSERVALASPGLU
7   VALVALLYSTHRGLNHISILELEUASPGLY
8   LYSVALILEASPPROLYSARGALAILEPRO
9   ARGASPGLUGLNASPLYSTHRGLYLYSILE
10   PHEVALGLYGLYILEGLYPROASPVALARG
11   PROLYSGLUPHEGLUGLUPHEPHESERGLN
12   TRPGLYTHRILEILEASPALAGLNLEUMET
13   LEUASPLYSASPTHRGLYGLNSERARGGLY
14   PHEGLYPHEVALTHRTYRASPSERALAASP
15   ALAVALASPARGVALCYSGLNASNLYSPHE
16   ILEASPPHELYSASPARGLYSILEGLUILE
17   LYSARGALAGLUPROARGHIS

Samples:

sample_1: rna15p, [U-100% 15N], 0.4 ± 0.04 mM; hrp1p 0.4 ± 0.04 mM; anchor RNA 0.4 ± 0.04 mM; H2O 93%; D2O 7%; NaCl 150 mM; Phosphate 20 mM

sample_2: rna15p 0.6 ± 0.02 mM; hrp1p, [U-100% 15N], 0.6 ± 0.07 mM; anchor RNA 0.6 ± 0.03 mM; H2O 93%; D2O 7%; NaCl 150 mM; Phosphate 20 mM

sample_3: rna15p, [U-100% 13C], 0.35 ± 0.03 mM; hrp1p, [U-100% 15N], 0.35 ± 0.03 mM; anchor RNA 0.35 ± 0.03 mM; H2O 93%; D2O 7%; NaCl 150 mM; Phosphate 20 mM

sample_4: rna15p, [U-100% 15N], 0.5 ± 0.05 mM; hrp1p, [U-100% 13C], 0.5 ± 0.05 mM; anchor RNA 0.5 ± 0.05 mM; H2O 93%; D2O 7%; NaCl 150 mM; Phosphate 20 mM

sample_5: rna15p, [U-100% 13C; U-100% 15N], 0.5 ± 0.04 mM; hrp1p 0.5 ± 0.04 mM; anchor RNA 0.5 ± 0.04 mM; H2O 93%; D2O 7%; NaCl 150 mM; Phosphate 20 mM

sample_6: rna15p 0.5 ± 0.02 mM; hrp1p, [U-100% 13C; U-100% 15N], 0.5 ± 0.02 mM; anchor RNA 0.5 ± 0.02 mM; H2O 93%; D2O 7%; NaCl 150 mM; Phosphate 20 mM

sample_conditions_1: ionic strength: 160 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3anisotropicsample_conditions_1
2D 1H-15N HSQCsample_4anisotropicsample_conditions_1
2D 1H-13C HSQCsample_3anisotropicsample_conditions_1
2D 1H-13C HSQCsample_4anisotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
3D HNCOsample_5isotropicsample_conditions_1
3D HNCAsample_5isotropicsample_conditions_1
3D HNCACBsample_5isotropicsample_conditions_1
3D HN(CO)CAsample_5isotropicsample_conditions_1
3D CBCA(CO)NHsample_5isotropicsample_conditions_1
3D HCCH-TOCSYsample_5isotropicsample_conditions_1
3D 1H-15N TOCSYsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_5isotropicsample_conditions_1
3D 1H-13C NOESYsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_6isotropicsample_conditions_1
3D 1H-13C NOESYsample_6isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

SPARKY, Goddard - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 750 MHz

Related Database Links:

PDB
DBJ GAA23344 GAA26207
EMBL CAA96746 CAY79715 CAA64546 CAA99142 CAY86168
GB AAA34984 AHY79328 AJP38746 AJR76066 AJR76567 AAA79097 AAB18142 AHY77195 EDN63753 EDV10496
REF NP_011471 NP_014518 XP_011105369
SP P25299 Q99383
TPG DAA08056 DAA10661
AlphaFold P25299 Q99383

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks