BMRB Entry 16266

Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16266

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Title:
Solution Structure of RPP29-RPP21 complex from Pyrococcus furiosis
Deposition date:
2009-04-28
Original release date:
2009-09-11
Authors:
Xu, Yiren; Foster, Mark
Citation:

Citation: Xu, Yiren; Amero, Carlos; Pulukkunat, Dileep; Gopalan, Venkat; Foster, Mark. "Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions."  J. Mol. Biol. 393, 1043-1055 (2009).
PubMed: 19733182

Assembly members:

Assembly members:
Pfu_RPP29, polymer, 127 residues, 14953.2 Da.
Pfu_RPP21, polymer, 123 residues, 14751.8 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Pyrococcus furiosus   Taxonomy ID: 2261   Superkingdom: Eukaryota   Kingdom: not available   Genus/species: Pyrococcus furiosus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET33b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Pfu_RPP29: MWRNSEERENRTSGRSQGSY QEIIGRTWIFRGAHRGRVNK KNIVWHELIGLKVRVVNSTH PGYVGIEGYVIDETRNMLVI AGENKVWKVPKDVCIFEFET WDGTKIKISGEKLVGRPEMR LKKRWRK
Pfu_RPP21: MAKYNEKKEKKRIAKERIDI LFSLAERVFPYSPELAKRYV ELALLVQQKAKVKIPRKWKR RYCKKCHAFLVPGINARVRL RQKRMPHIVVKCLECGHIMR YPYIKEIKKRRIEKMEYGGL VPR

Data sets:
Data typeCount
13C chemical shifts490
15N chemical shifts114
1H chemical shifts744

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Subunit 11
2Subunit 22
3ZINC ION3

Entities:

Entity 1, Subunit 1 127 residues - 14953.2 Da.

Residues 1-18 are not present in the solution structure ensemble.

1   METTRPARGASNSERGLUGLUARGGLUASN
2   ARGTHRSERGLYARGSERGLNGLYSERTYR
3   GLNGLUILEILEGLYARGTHRTRPILEPHE
4   ARGGLYALAHISARGGLYARGVALASNLYS
5   LYSASNILEVALTRPHISGLULEUILEGLY
6   LEULYSVALARGVALVALASNSERTHRHIS
7   PROGLYTYRVALGLYILEGLUGLYTYRVAL
8   ILEASPGLUTHRARGASNMETLEUVALILE
9   ALAGLYGLUASNLYSVALTRPLYSVALPRO
10   LYSASPVALCYSILEPHEGLUPHEGLUTHR
11   TRPASPGLYTHRLYSILELYSILESERGLY
12   GLULYSLEUVALGLYARGPROGLUMETARG
13   LEULYSLYSARGTRPARGLYS

Entity 2, Subunit 2 123 residues - 14751.8 Da.

Residues 1-8 and 106-123 are not present in the solution structure ensemble. Last six residues are leftover after cleavage of His-tag.

1   METALALYSTYRASNGLULYSLYSGLULYS
2   LYSARGILEALALYSGLUARGILEASPILE
3   LEUPHESERLEUALAGLUARGVALPHEPRO
4   TYRSERPROGLULEUALALYSARGTYRVAL
5   GLULEUALALEULEUVALGLNGLNLYSALA
6   LYSVALLYSILEPROARGLYSTRPLYSARG
7   ARGTYRCYSLYSLYSCYSHISALAPHELEU
8   VALPROGLYILEASNALAARGVALARGLEU
9   ARGGLNLYSARGMETPROHISILEVALVAL
10   LYSCYSLEUGLUCYSGLYHISILEMETARG
11   TYRPROTYRILELYSGLUILELYSLYSARG
12   ARGILEGLULYSMETGLUTYRGLYGLYLEU
13   VALPROARG

Entity 3, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Pfu RPP29, [U-100% 13C; U-100% 15N], 1.25 mM; Pfu RPP21 1.5 mM; TRIS 10 mM; potassium chloride 10 mM; Zinc chloride 0.3 mM; sodium azide 0.02%; D2O, [U-99.8% 2H], 10%; H2O 90%; DSS 3 mM

sample_2: Pfu RPP29, [U-100% 13C; U-100% 15N], 1.25 mM; Pfu RPP21 1.5 mM; TRIS 10 mM; potassium chloride 10 mM; Zinc chloride 0.3%; sodium azide 0.02%; D2O, [U-99.8% 2H], 100%; DSS 3 mM

sample_3: Pfu RPP21, [U-100% 13C; U-100% 15N], 1 mM; Pfu RPP29 1.2 mM; TRIS 10 mM; potassium chloride 10 mM; Zinc chloride 0.3 mM; sodium azide 0.02%; H2O 90%; D2O, [U-99.8% 2H], 10%; DSS 3 mM

sample_4: Pfu RPP21, [U-100% 13C; U-100% 15N], 1 mM; Pfu RPP29 1.2 mM; TRIS 10 mM; potassium chloride 10 mM; Zinc chloride 0.3 mM; sodium azide 0.02%; D2O, [U-99.8% 2H], 100%; DSS 3 mM

sample_conditions_1: ionic strength: 0.047 M; pH: 5.8; pressure: 1 atm; temperature: 328 K

sample_conditions_2: ionic strength: 0.047 M; pH: 6.21; pressure: 1 atm; temperature: 328 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D C(CO)NH TOCSYsample_1isotropicsample_conditions_1
3D C(CO)NH TOCSYsample_3isotropicsample_conditions_1
3D H(C)(CO)NH TOCSYsample_1isotropicsample_conditions_1
3D H(C)(CO)NH TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_2
3D 1H-13C NOESYsample_4isotropicsample_conditions_2
3D 13C-filtered/edited NOESYsample_2isotropicsample_conditions_2
3D 13C-filtered/edited NOESYsample_4isotropicsample_conditions_2

Software:

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing

NMRView, Johnson, One Moon Scientific - data analysis, peak picking

xwinnmr, Bruker Biospin - collection

CARA, Keller R., Wuthrich K. - chemical shift assignment, data analysis

SANE, Duggan, Legge, Dyson & Wright - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - data analysis, refinement, structure solution

NMR spectrometers:

  • Bruker DMX 600 MHz
  • Bruker DMX 800 MHz

Related Database Links:

BMRB 15935 15776 15935
PDB
GB AAL81940 AAL81737 AFN05027
REF WP_048059096 NP_579342 WP_011012760 YP_006493319
SP Q8U007 Q8U0H6
AlphaFold Q8U007 Q8U0H6

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