BMRB Entry 19778

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19778
MolProbity Validation Chart

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Title:
Structural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) 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:
CPEB1RRM12, polymer, 213 residues, 23930.746 Da.
5'-UUUUA-3', polymer, 5 residues, 1508.924 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):
CPEB1RRM12: MTWSGQLPPRNYKNPIYSCK VFLGGVPWDITEAGLVNTFR VFGSLSVEWPGKDGKHPRCP PKGYVYLVFELEKSVRSLLQ ACSHDPLSPDGLSEYYFKMS SRRMRCKEVQVIPWVLADSN FVRSPSQRLDPSRTVFVGAL HGMLNAEALAAILNDLFGGV VYAGIDTDKHKYPIGSGRVT FNNQRSYLKAVSAAFVEIKT TKFTKKVQIDPYL
5'-UUUUA-3': UUUUA

Data sets:
Data typeCount

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1CPEB1RRM121
2RNA (5'-R(*UP*UP*UP*UP*A)-3')2

Entities:

Entity 1, CPEB1RRM12 213 residues - 23930.746 Da.

1   METTHRTRPSERGLYGLNLEUPROPROARG
2   ASNTYRLYSASNPROILETYRSERCYSLYS
3   VALPHELEUGLYGLYVALPROTRPASPILE
4   THRGLUALAGLYLEUVALASNTHRPHEARG
5   VALPHEGLYSERLEUSERVALGLUTRPPRO
6   GLYLYSASPGLYLYSHISPROARGCYSPRO
7   PROLYSGLYTYRVALTYRLEUVALPHEGLU
8   LEUGLULYSSERVALARGSERLEULEUGLN
9   ALACYSSERHISASPPROLEUSERPROASP
10   GLYLEUSERGLUTYRTYRPHELYSMETSER
11   SERARGARGMETARGCYSLYSGLUVALGLN
12   VALILEPROTRPVALLEUALAASPSERASN
13   PHEVALARGSERPROSERGLNARGLEUASP
14   PROSERARGTHRVALPHEVALGLYALALEU
15   HISGLYMETLEUASNALAGLUALALEUALA
16   ALAILELEUASNASPLEUPHEGLYGLYVAL
17   VALTYRALAGLYILEASPTHRASPLYSHIS
18   LYSTYRPROILEGLYSERGLYARGVALTHR
19   PHEASNASNGLNARGSERTYRLEULYSALA
20   VALSERALAALAPHEVALGLUILELYSTHR
21   THRLYSPHETHRLYSLYSVALGLNILEASP
22   PROTYRLEU

Entity 2, RNA (5'-R(*UP*UP*UP*UP*A)-3') 5 residues - 1508.924 Da.

1   UUUUA

Samples:

sample_1: CPEB1RRM12, [U-100% 13C; U-100% 15N; U-80% 2H], 0.4 – 0.6 mM; 5'-UUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DTT 1 mM; magnesium sulfate 1 mM; D2O 10%; H2O 90%

sample_2: CPEB1RRM12, [U-100% 13C; U-100% 15N], 0.4 – 0.6 mM; 5'-UUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DTT 1 mM; magnesium sulfate 1 mM; D2O 10%; H2O 90%

sample_3: CPEB1RRM12, [U-100% 13C; U-100% 15N], 0.4 – 0.6 mM; 5'-UUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DTT 1 mM; magnesium sulfate 1 mM; D2O 100%

sample_4: CPEB1RRM12, [U-100% 15N], 0.4 – 0.6 mM; 5'-UUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DTT 1 mM; magnesium sulfate 1 mM; D2O 10%; H2O 90%

sample_5: CPEB1RRM12, [U-100% 15N], 0.4 – 0.6 mM; 5'-UUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DTT 1 mM; magnesium sulfate 1 mM; D2O 100%

sample_6: CPEB1RRM12, [U-100% 15N], 0.4 – 0.6 mM; 5'-CUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DTT 1 mM; magnesium sulfate 1 mM; D2O 100%

sample_7: CPEB1RRM12, [U-100% 13C; U-100% 15N], 0.4 – 0.6 mM; 5'-CUUUA-3'0.4 – 0.6 mM; sodium chloride 100 mM; sodium phosphate 50 mM; DTT 1 mM; magnesium sulfate 1 mM; D2O 100%

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 313 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D TROSYsample_4isotropicsample_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_5isotropicsample_conditions_1
3D trHNCAsample_1isotropicsample_conditions_1
3D trHN(CO)CAsample_1isotropicsample_conditions_1
3D trCBCA(CO)NHsample_1isotropicsample_conditions_1
3D trHNCACBsample_1isotropicsample_conditions_1
3D trHNCACOsample_1isotropicsample_conditions_1
3D trHNCOsample_1isotropicsample_conditions_1
3D hCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCcH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 13C-F1-filtered F2-filtered NOESYsample_6isotropicsample_conditions_1
2D 1H-1H F1-13C-filtered F2-13C-edited NOESYsample_6isotropicsample_conditions_1
3D 13C-F1-edited F3-filtered NOESY HSQCsample_6isotropicsample_conditions_1

Software:

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

TOPSPIN, Bruker Biospin - processing

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

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

Related Database Links:

BMRB 19775
PDB
DBJ BAB14496 BAE87429 BAG63194 BAH11723 BAH13212
EMBL CAH92427
GB AAH35348 AAH50629 AAK01239 AAK01240 ADQ32841
REF NP_001073001 NP_001073002 NP_001073003 NP_001126432 NP_001239455
SP Q5R733 Q9BZB8
TPG DAA17635
AlphaFold Q5R733 Q9BZB8

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