BMRB Entry 19726

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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/BMR19726
MolProbity Validation Chart

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Title:
Protein-RNA structure
Deposition date:
2014-01-09
Original release date:
2014-05-27
Authors:
Daubner, Gerrit; Allain, Frederic
Citation:

Citation: Daubner, Gerrit; Bruemmer, Anneke; Tocchini, Cristina; Gerhardy, Stefan; Ciosk, Rafal; Zavolan, Mihaela; Allain, Frederic. "Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1"  .

Assembly members:

Assembly members:
GermLine_development_Defective_1, polymer, 142 residues, 16075.667 Da.
5'-CUACUCAUAU-3', polymer, 10 residues, 3082.892 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: Caenorhabditis elegans

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pTYB1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GermLine_development_Defective_1: LPEPAGDMISITEKIYVPKN EYPDYNFVGRILGPRGMTAK QLEQDTGCKIMVRGKGSMRD KSKESAHRGKANWEHLEDDL HVLVQCEDTENRVHIKLQAA LEQVKKLLIPAPEGTDELKR KQLMELAIINGTYRPMKSPN PA
5'-CUACUCAUAU-3': CUACUCAUAU

Data sets:
Data typeCount
13C chemical shifts386
15N chemical shifts144
1H chemical shifts1010

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1GLD-1 KH-QUA2 bound to 5'-CUACUCAUAU-3'1
2RNA2

Entities:

Entity 1, GLD-1 KH-QUA2 bound to 5'-CUACUCAUAU-3' 142 residues - 16075.667 Da.

1   LEUPROGLUPROALAGLYASPMETILESER
2   ILETHRGLULYSILETYRVALPROLYSASN
3   GLUTYRPROASPTYRASNPHEVALGLYARG
4   ILELEUGLYPROARGGLYMETTHRALALYS
5   GLNLEUGLUGLNASPTHRGLYCYSLYSILE
6   METVALARGGLYLYSGLYSERMETARGASP
7   LYSSERLYSGLUSERALAHISARGGLYLYS
8   ALAASNTRPGLUHISLEUGLUASPASPLEU
9   HISVALLEUVALGLNCYSGLUASPTHRGLU
10   ASNARGVALHISILELYSLEUGLNALAALA
11   LEUGLUGLNVALLYSLYSLEULEUILEPRO
12   ALAPROGLUGLYTHRASPGLULEULYSARG
13   LYSGLNLEUMETGLULEUALAILEILEASN
14   GLYTHRTYRARGPROMETLYSSERPROASN
15   PROALA

Entity 2, RNA 10 residues - 3082.892 Da.

1   CUACUCAUAU

Samples:

15N: GLD-1 (aa 195-336), [U-15N], 0.45 mM; 5'-CUACUCAUAU-3' 0.45 mM; sodium chloride 50 mM; sodium phosphate 20 mM; DTT 3 mM; H2O 90%; D2O, [U-100% 2H], 10%

15N_13C: GLD-1 (aa 195-336), [U-13C; U-15N], 0.45 mM; 5'-CUACUCAUAU-3' 0.45 mM; sodium chloride 50 mM; sodium phosphate 20 mM; DTT 3 mM; H2O 90%; D2O, [U-100% 2H], 10%

15N_(D2O): GLD-1 (aa 195-336), [U-15N], 0.45 mM; 5'-CUACUCAUAU-3' 0.45 mM; sodium chloride 50 mM; sodium phosphate 20 mM; DTT 3 mM; D2O, [U-100% 2H], 100%

15N_13C_(D2O): GLD-1 (aa 195-336), [U-13C; U-15N], 0.45 mM; 5'-CUACUCAUAU-3' 0.45 mM; sodium chloride 50 mM; sodium phosphate 20 mM; DTT 3 mM; D2O, [U-100% 2H], 100%

15N_13C_(10): GLD-1 (aa 195-336), [U-10% 13C; U-100% 15N], 0.45 mM; 5'-CUACUCAUAU-3' 0.45 mM; sodium chloride 50 mM; sodium phosphate 20 mM; DTT 3 mM; H2O 90%; D2O, [U-100% 2H], 10%

15N_(Phage): GLD-1 (aa 195-336), [U-15N], 0.45 mM; 5'-CUACUCAUAU-3' 0.45 mM; sodium chloride 50 mM; sodium phosphate 20 mM; DTT 3 mM; Pf1 phage 14 mg/mL; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 0.17 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15Nisotropicsample_conditions_1
2D 1H-13C HSQC15N_13C_(D2O)isotropicsample_conditions_1
3D HNCA15N_13Cisotropicsample_conditions_1
3D HN(CO)CA15N_13Cisotropicsample_conditions_1
3D HNCO15N_13Cisotropicsample_conditions_1
3D HN(CA)CO15N_13Cisotropicsample_conditions_1
3D CBCA(CO)NH15N_13Cisotropicsample_conditions_1
3D HCCH-TOCSY15N_13Cisotropicsample_conditions_1
3D 1H-15N NOESY15Nisotropicsample_conditions_1
3D 1H-13C NOESY15N_13Cisotropicsample_conditions_1
2D 1H-1H TOCSY15N_(D2O)isotropicsample_conditions_1
2D 1H-1H NOESY15N_(D2O)isotropicsample_conditions_1
2D F1f F2f 1H-1H NOESY15N_(D2O)isotropicsample_conditions_1
2D 1H-13C HSQC15Nisotropicsample_conditions_1
2D F2f 1H-1H NOESY15N_13C_(D2O)isotropicsample_conditions_1
3D F1f F2e 1H-1H NOESY15N_13C_(D2O)isotropicsample_conditions_1
Long-range 1H-15N HSQC15Nisotropicsample_conditions_1
3D HNHA15Nisotropicsample_conditions_1
2D 1H-15N IPAP HSQC15N_(Phage)anisotropicsample_conditions_1
2D 1H-13C HSQC15N_13C_(10)isotropicsample_conditions_1

Software:

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

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

SPARKY v3.114, Goddard - chemical shift assignment

TOPSPIN v3.0, Bruker Biospin - collection

TALOS v+, Cornilescu, Delaglio and Bax - collection

ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis

ATNOSCANDID v2.1, Herrmann, Guntert and Wuthrich - peak picking

PALES v2.1, Zweckstetter, Hummer and Bax - data analysis

WhatIF v10.1.1, Vriend - data analysis

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 750 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
EMBL CAB03417
GB AAC46632 EFP08647
PRF 2116296A
REF NP_492143 XP_003100676
SP Q17339
AlphaFold Q17339

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