BMRB Entry 19400

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19400
MolProbity Validation Chart

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Title:
The structure of the Box CD enzyme reveals regulation of rRNA methylation
Deposition date:
2013-07-31
Original release date:
2013-10-08
Authors:
Lapinaite, Audrone; Simon, B.; Skjaerven, L.; Rakwalska-bange, M.; Gabel, F.; Carlomagno, T.
Citation:

Citation: Lapinaite, Audrone; Simon, Bernd; Skjaerven, Lars; Rakwalska-Bange, Magdalena; Gabel, Frank; Carlomagno, Teresa. "The structure of the box C/D enzyme reveals regulation of RNA methylation."  Nature 502, 519-523 (2013).
PubMed: 24121435

Assembly members:

Assembly members:
SSR26, polymer, 72 residues, 23589.23362 Da.
NOP5-NOP56_RELATED_PROTEIN, polymer, 366 residues, 42138.6332 Da.
50S_RIBOSOMAL_PROTEIN_L7AE, polymer, 121 residues, 13175.4847 Da.
FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE, polymer, 227 residues, 25762.6891 Da.
5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', polymer, 11 residues, 3466.08516 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SSR26: GCGAGCAAUGAUGAGUGAUG GGCGAACUGAGCUCGAAAGA GCAAUGAUGAGUGAUGGGCG AACUGAGCUCGC
NOP5-NOP56_RELATED_PROTEIN: FISENVRGIYAFDENGNLIE KRYFTDKPEKVLDQLLKGEI TKDLEELLNSLKEKGYDEFV FEHPCLSRRAKELGFSATTE FPNIAGERLRSNPCEFLGEN WFEEYYKVGVALTRMRIQEQ SGARDKMVIQAIEALDDVDK VINLLVARLREWYSLHFPEL DELLPKHPQYVAFVKTVGHR DNINEEVLRCLGLSECKIKK ILEAKEKTMGAWMDQTDIEV VRQLAEEIDRLYQLRKKLED YIDRAMCDVAPNLKALVGAK LAARLISLAGGLRELAMMPS STIQVLGAEKALFRHLRTGA KPPKHGVIYQYPAINRSPWW QRGKIARALAGKLAIAARVD YFCGEYIAEELKKELEARIR EIKEKY
50S_RIBOSOMAL_PROTEIN_L7AE: KPSYVKFEVPKCLAEKALQA VEIARDTGKIRKGTNETTKA VERGCAKLVIIAEDVDPEEI VAHLPPLCEECEIPYIYVPC KKELGAAACIEVAAASVAII EPGKARDLVEEIAMKVKELM K
FIBRILLARIN-LIKE_RRNA-TRNA_2'-O-METHYLTRANSFERASE: MVEVKKHKFPGVYVVIDDDG SEKIATKNLVPGQRVYGERV IKWEGEEYRIWNPHRSKLGA AIVNGLKNFPIKPGKSVLYL GIASGTTASHVSDIVGWEGK IYGIEFSPRVLRELVPIVEE RRNIIPILGDATKPEEYRAL VTKVDVIFEDVAQPTQAKIL IDNAKAYLKRGGYGMIAVKS RSIDVTKEPEQVFKEVEREL SEYFEVIERLNLEPYEKDHA LFVVRKP
5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3': UCGCCCAUCAC

Data sets:
Data typeCount
13C chemical shifts79
1H chemical shifts240

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1SSR26, 11
2SSR26, 21
3NOP5/NOP56 RELATED PROTEIN, 12
450S RIBOSOMAL PROTEIN L7AE, 13
5FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 14
6NOP5/NOP56 RELATED PROTEIN, 22
750S RIBOSOMAL PROTEIN L7AE, 23
8FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 24
9NOP5/NOP56 RELATED PROTEIN, 32
1050S RIBOSOMAL PROTEIN L7AE, 33
11FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 34
12NOP5/NOP56 RELATED PROTEIN, 42
1350S RIBOSOMAL PROTEIN L7AE, 43
14FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 44
155'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 15
165'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 25
175'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 35
185'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 45

Entities:

Entity 1, SSR26, 1 72 residues - 23589.23362 Da.

1   GCGAGCAAUG
2   AUGAGUGAUG
3   GGCGAACUGA
4   GCUCGAAAGA
5   GCAAUGAUGA
6   GUGAUGGGCG
7   AACUGAGCUC
8   GC

Entity 2, NOP5/NOP56 RELATED PROTEIN, 1 366 residues - 42138.6332 Da.

1   PHEILESERGLUASNVALARGGLYILETYR
2   ALAPHEASPGLUASNGLYASNLEUILEGLU
3   LYSARGTYRPHETHRASPLYSPROGLULYS
4   VALLEUASPGLNLEULEULYSGLYGLUILE
5   THRLYSASPLEUGLUGLULEULEUASNSER
6   LEULYSGLULYSGLYTYRASPGLUPHEVAL
7   PHEGLUHISPROCYSLEUSERARGARGALA
8   LYSGLULEUGLYPHESERALATHRTHRGLU
9   PHEPROASNILEALAGLYGLUARGLEUARG
10   SERASNPROCYSGLUPHELEUGLYGLUASN
11   TRPPHEGLUGLUTYRTYRLYSVALGLYVAL
12   ALALEUTHRARGMETARGILEGLNGLUGLN
13   SERGLYALAARGASPLYSMETVALILEGLN
14   ALAILEGLUALALEUASPASPVALASPLYS
15   VALILEASNLEULEUVALALAARGLEUARG
16   GLUTRPTYRSERLEUHISPHEPROGLULEU
17   ASPGLULEULEUPROLYSHISPROGLNTYR
18   VALALAPHEVALLYSTHRVALGLYHISARG
19   ASPASNILEASNGLUGLUVALLEUARGCYS
20   LEUGLYLEUSERGLUCYSLYSILELYSLYS
21   ILELEUGLUALALYSGLULYSTHRMETGLY
22   ALATRPMETASPGLNTHRASPILEGLUVAL
23   VALARGGLNLEUALAGLUGLUILEASPARG
24   LEUTYRGLNLEUARGLYSLYSLEUGLUASP
25   TYRILEASPARGALAMETCYSASPVALALA
26   PROASNLEULYSALALEUVALGLYALALYS
27   LEUALAALAARGLEUILESERLEUALAGLY
28   GLYLEUARGGLULEUALAMETMETPROSER
29   SERTHRILEGLNVALLEUGLYALAGLULYS
30   ALALEUPHEARGHISLEUARGTHRGLYALA
31   LYSPROPROLYSHISGLYVALILETYRGLN
32   TYRPROALAILEASNARGSERPROTRPTRP
33   GLNARGGLYLYSILEALAARGALALEUALA
34   GLYLYSLEUALAILEALAALAARGVALASP
35   TYRPHECYSGLYGLUTYRILEALAGLUGLU
36   LEULYSLYSGLULEUGLUALAARGILEARG
37   GLUILELYSGLULYSTYR

Entity 3, 50S RIBOSOMAL PROTEIN L7AE, 1 121 residues - 13175.4847 Da.

1   LYSPROSERTYRVALLYSPHEGLUVALPRO
2   LYSCYSLEUALAGLULYSALALEUGLNALA
3   VALGLUILEALAARGASPTHRGLYLYSILE
4   ARGLYSGLYTHRASNGLUTHRTHRLYSALA
5   VALGLUARGGLYCYSALALYSLEUVALILE
6   ILEALAGLUASPVALASPPROGLUGLUILE
7   VALALAHISLEUPROPROLEUCYSGLUGLU
8   CYSGLUILEPROTYRILETYRVALPROCYS
9   LYSLYSGLULEUGLYALAALAALACYSILE
10   GLUVALALAALAALASERVALALAILEILE
11   GLUPROGLYLYSALAARGASPLEUVALGLU
12   GLUILEALAMETLYSVALLYSGLULEUMET
13   LYS

Entity 4, FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, 1 227 residues - 25762.6891 Da.

1   METVALGLUVALLYSLYSHISLYSPHEPRO
2   GLYVALTYRVALVALILEASPASPASPGLY
3   SERGLULYSILEALATHRLYSASNLEUVAL
4   PROGLYGLNARGVALTYRGLYGLUARGVAL
5   ILELYSTRPGLUGLYGLUGLUTYRARGILE
6   TRPASNPROHISARGSERLYSLEUGLYALA
7   ALAILEVALASNGLYLEULYSASNPHEPRO
8   ILELYSPROGLYLYSSERVALLEUTYRLEU
9   GLYILEALASERGLYTHRTHRALASERHIS
10   VALSERASPILEVALGLYTRPGLUGLYLYS
11   ILETYRGLYILEGLUPHESERPROARGVAL
12   LEUARGGLULEUVALPROILEVALGLUGLU
13   ARGARGASNILEILEPROILELEUGLYASP
14   ALATHRLYSPROGLUGLUTYRARGALALEU
15   VALTHRLYSVALASPVALILEPHEGLUASP
16   VALALAGLNPROTHRGLNALALYSILELEU
17   ILEASPASNALALYSALATYRLEULYSARG
18   GLYGLYTYRGLYMETILEALAVALLYSSER
19   ARGSERILEASPVALTHRLYSGLUPROGLU
20   GLNVALPHELYSGLUVALGLUARGGLULEU
21   SERGLUTYRPHEGLUVALILEGLUARGLEU
22   ASNLEUGLUPROTYRGLULYSASPHISALA
23   LEUPHEVALVALARGLYSPRO

Entity 5, 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3', 1 11 residues - 3466.08516 Da.

1   UCGCCCAUCA
2   C

Samples:

sample_1: SSR260.014 – 0.03 mM; NOP5/NOP56 RELATED PROTEIN0.014 – 0.03 mM; 50S RIBOSOMAL PROTEIN L7AE0.014 – 0.03 mM; FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE, [U-13C], 0.014 – 0.03 mM; 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3'0.014 – 0.03 mM

sample_conditions_1: ionic strength: 0.0 mM; pH: 6.600; pressure: 1 atm; temperature: 328.000 K

Experiments:

NameSampleSample stateSample conditions
13C,1H-HMQCsample_1solutionsample_conditions_1

Software:

AutoDep v4.3 - chemical shift assignment

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - chemical shift assignment

NMRView vany - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

PDB
UNP Q8U4M1_PYRFU RL7A_PYRFU FLPA_PYRFU
GB AAL80184 AFN04514 AAL80183 AFN04515
REF WP_011011172 WP_011011171
SP Q8U4M2
AlphaFold Q8U4M2 Q8U160 G0EDH5 Q8U4M2