BMRB Entry 19776

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19776
MolProbity Validation Chart

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Title:
Solution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 4 (CPEB4) in complex with RNA
Deposition date:
2014-02-07
Original release date:
2014-07-21
Authors:
Afroz, Tariq; Skrisovska, Lenka; Belloc, Eulalia; Boixet, Jordina; Mendez, Raul; Allain, Frederic
Citation:

Citation: Afroz, Tariq; Skrisovska, Lenka; Belloc, Eulalia; Boixet, Jordina; Mendez, Raul; Allain, Frederic. "A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins"  Genes Dev. 28, 1498-1514 (2014).
PubMed: 24990967

Assembly members:

Assembly members:
CPEB4RRM12, polymer, 203 residues, 22826.154 Da.
RNA_(5'-CUUUA)-3'), polymer, 5 residues, 1507.939 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28A(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CPEB4RRM12: SHQNGERVERYSRKVFVGGL PPDIDEDEITASFRRFGPLI VDWPHKAESKSYFPPKGYAF LLFQDESSVQALIDACIEED GKLYLCVSSPTIKDKPVQIR PWNLSDSDFVMDGSQPLDPR KTIFVGGVPRPLRAVELAMI MDRLYGGVCYAGIDTDPELK YPKGAGRVAFSNQQSYIAAI SARFVQLQHGEIDKRVEVKP YVL
RNA_(5'-CUUUA)-3'): CUUUA

Data sets:
Data typeCount
13C chemical shifts521
15N chemical shifts177
1H chemical shifts1147

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CPEB4RRM121
2RNA (5'-R(*CP*UP*UP*UP*A)-3')2

Entities:

Entity 1, CPEB4RRM12 203 residues - 22826.154 Da.

1   SERHISGLNASNGLYGLUARGVALGLUARG
2   TYRSERARGLYSVALPHEVALGLYGLYLEU
3   PROPROASPILEASPGLUASPGLUILETHR
4   ALASERPHEARGARGPHEGLYPROLEUILE
5   VALASPTRPPROHISLYSALAGLUSERLYS
6   SERTYRPHEPROPROLYSGLYTYRALAPHE
7   LEULEUPHEGLNASPGLUSERSERVALGLN
8   ALALEUILEASPALACYSILEGLUGLUASP
9   GLYLYSLEUTYRLEUCYSVALSERSERPRO
10   THRILELYSASPLYSPROVALGLNILEARG
11   PROTRPASNLEUSERASPSERASPPHEVAL
12   METASPGLYSERGLNPROLEUASPPROARG
13   LYSTHRILEPHEVALGLYGLYVALPROARG
14   PROLEUARGALAVALGLULEUALAMETILE
15   METASPARGLEUTYRGLYGLYVALCYSTYR
16   ALAGLYILEASPTHRASPPROGLULEULYS
17   TYRPROLYSGLYALAGLYARGVALALAPHE
18   SERASNGLNGLNSERTYRILEALAALAILE
19   SERALAARGPHEVALGLNLEUGLNHISGLY
20   GLUILEASPLYSARGVALGLUVALLYSPRO
21   TYRVALLEU

Entity 2, RNA (5'-R(*CP*UP*UP*UP*A)-3') 5 residues - 1507.939 Da.

1   CUUUA

Samples:

sample_1: sodium phosphate 50 mM; sodium chloride 100 mM; DTT 1 mM; CPEB4RRM12, [U-100% 13C; U-100% 15N], 0.6 mM; 5'-CUUUA-3' 0.6 mM; H2O 90%; D2O 10%

sample_2: CPEB4RRM12, [U-100% 13C; U-100% 15N], 0.4 – 0.6 mM; RNA (5'-CUUUA)-3')0.4 – 0.6 mM; sodium chloride 100 mM; DTT 1 mM; sodium phosphate 50 mM; D2O 100%

sample_3: CPEB4RRM12, [U-100% 13C; U-100% 15N; U-80% 2H], 0.4 – 0.6 mM; 5'-CUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; DTT 1 mM; sodium phosphate 50 mM; H2O 90%; D2O 10%

sample_4: CPEB4RRM12, [U-100% 15N], 0.4 – 0.6 mM; 5'-CUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; DTT 1 mM; potassium phosphate 50 mM; D2O 100%

sample_5: CPEB4RRM12, [U-100% 15N], 0.4 – 0.6 mM; 5'-CUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; DTT 1 mM; potassium phosphate 50 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.15 M; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_5isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
3D trHNCAsample_3isotropicsample_conditions_1
3D trHN(CO)CAsample_3isotropicsample_conditions_1
3D trCBCA(CO)NHsample_3isotropicsample_conditions_1
3D trHNCACBsample_3isotropicsample_conditions_1
3D trHNCOsample_3isotropicsample_conditions_1
3D trHCACOsample_3isotropicsample_conditions_1
3D HCcH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_5isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_3isotropicsample_conditions_1
3D hCCH TOCSYsample_3isotropicsample_conditions_1
2D 1H-15N TROSYsample_5isotropicsample_conditions_1
2D 13C F1-filtered F2-filtered NOESYsample_1isotropicsample_conditions_1
2D 1H-1H F1-13C-filtered F2-13C-edited NOESYsample_1isotropicsample_conditions_1
3D 13C F1-edited, F3-filtered NOESY HSQCsample_1isotropicsample_conditions_1

Software:

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

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

Related Database Links:

BMRB 19777
PDB
DBJ BAA76784 BAB21764 BAB29821 BAB29832 BAC41458
EMBL CAD98072 CAF91663 CAG10148 CAH91098 CAH91116
GB AAH36444 AAH36899 AAH55522 AAI03940 AAI03941
REF NP_001015925 NP_001100462 NP_001170850 NP_001170852 NP_001170853
SP Q17RY0 Q28CH2 Q7SXN4 Q7TN98 Q7TN99
TPG DAA14951 DAA18039 DAA28393 DAA28394 DAA28395
AlphaFold Q17RY0 Q28CH2 Q7SXN4 Q7TN98 Q7TN99

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