BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19609

Title: Solution Structure of Protein-RNA Ternary Complex

Authors: Takahashi, Mari; Kuwasako, Kanako; Unzai, Satoru; Tsuda, Kengo; Yoshikawa, Seiko; He, Fahu; Kobayashi, Naohiro; Guntert, Peter; Shirouzu, Mikako; Ito, Takuhiro; Tanaka, Akiko; Yokoyama, Shigeyuki; Hagiwara, Masatoshi; Kuroyanagi, Hidehito; Muto, Yutaka

Citation: Kuwasako, Kanako; Takahashi, Mari; Unzai, Satoru; Tsuda, Kengo; Yoshikawa, Seiko; He, Fahu; Kobayashi, Naohiro; Guntert, Peter; Shirouzu, Mikako; Ito, Takuhiro; Tanaka, Akiko; Yokoyama, Shigeyuki; Hagiwara, Masatoshi; Kuroyanagi, Hidehito; Muto, Yutaka. "Solution Structure of Protein-RNA Ternary Complex"  Not known ., .-..

Assembly members:
entity_1, polymer, 94 residues, 10588.121 Da.
entity_2, polymer, 105 residues, 11611.109 Da.
RNA, polymer, 12 residues, Formula weight is not available

Natural source:   Common Name: nematode   Taxonomy ID: 6239   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Caenorhabditis elegans

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

Entity Sequences (FASTA):
entity_1: GDGPRRLHVSNIPFKYREPD LTAMFEKVGPVVDVEIIFNE RGSKGFGFVTMQNPDDADRA RAEFNGTTIEGRRVEVNLAT QRVHNKKAKPLMSV
entity_2: GSTNAEPVVGSRDTMFTKIF VGGLPYHTSDKTLHEYFEQF GDIEEAVVITDRNTQKSRGY GFVTMKDRASAERACKDPNP IIDGRKANVNLAYLGAKPRT NVQLA
RNA: UGCAUGGUGUGC

Data sets:
Data typeCount
13C chemical shifts575
15N chemical shifts184
1H chemical shifts1157

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3RNA3

Entities:

Entity 1, entity_1 94 residues - 10588.121 Da.

1   GLYASPGLYPROARGARGLEUHISVALSER
2   ASNILEPROPHELYSTYRARGGLUPROASP
3   LEUTHRALAMETPHEGLULYSVALGLYPRO
4   VALVALASPVALGLUILEILEPHEASNGLU
5   ARGGLYSERLYSGLYPHEGLYPHEVALTHR
6   METGLNASNPROASPASPALAASPARGALA
7   ARGALAGLUPHEASNGLYTHRTHRILEGLU
8   GLYARGARGVALGLUVALASNLEUALATHR
9   GLNARGVALHISASNLYSLYSALALYSPRO
10   LEUMETSERVAL

Entity 2, entity_2 105 residues - 11611.109 Da.

1   GLYSERTHRASNALAGLUPROVALVALGLY
2   SERARGASPTHRMETPHETHRLYSILEPHE
3   VALGLYGLYLEUPROTYRHISTHRSERASP
4   LYSTHRLEUHISGLUTYRPHEGLUGLNPHE
5   GLYASPILEGLUGLUALAVALVALILETHR
6   ASPARGASNTHRGLNLYSSERARGGLYTYR
7   GLYPHEVALTHRMETLYSASPARGALASER
8   ALAGLUARGALACYSLYSASPPROASNPRO
9   ILEILEASPGLYARGLYSALAASNVALASN
10   LEUALATYRLEUGLYALALYSPROARGTHR
11   ASNVALGLNLEUALA

Entity 3, RNA 12 residues - Formula weight is not available

1   UGCAUGGUGU
2   GC

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.7 mM; entity_2, [U-99% 13C; U-99% 15N], 0.7 mM; RNA 0.7 mM; H2O 90%; D2O 10%; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%

sample_conditions_1: ionic strength: 0.1 M; pH: 6; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz

Related Database Links:

BMRB 19680 19686 11541 18845 18846 19653
PDB
EMBL CAA85276 CAD82915 CCU83325 CCD71425 CCD71429
GB ABF22491 EFO82252 EGT29982 ETN82682 KHJ75674 KIH66793
REF NP_001293646 NP_497841 NP_871667 NP_001129938 NP_508674 XP_003117654 XP_006219866