BMRB Entry 30570

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR30570
MolProbity Validation Chart

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Title:
NMR solution structure of Bcd1p120-303 from Saccharomyces cerevisiae
Deposition date:
2019-02-12
Original release date:
2020-08-14
Authors:
Bragantini, B.; Quinternet, M.; Charpentier, B.; Manival, X.
Citation:

Citation: Bragantini, Benoit; Charron, Christophe; Bourguet, Maxime; Paul, Arnaud; Tiotiu, Decebal; Rothe, Benjamin; Marty, Helene; Terral, Guillaume; Hessmann, Steve; Decourty, Laurence; Chagot, Marie-Eve; Strub, Jean-Marc; Massenet, Severine; Bertrand, Edouard; Quinternet, Marc; Saveanu, Cosmin; Cianferani, Sarah; Labialle, Stephane; Manival, Xavier; Charpentier, Bruno. "The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity"  Nat. Commun. 12, 1859-1859 (2021).
PubMed: 33767140

Assembly members:

Assembly members:
entity_1, polymer, 188 residues, 21864.262 Da.

Natural source:

Natural source:   Common Name: Baker's yeast   Taxonomy ID: 559292   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPHMRDSTECQRIIRRGVNC LMLPKGMQRSSQNRSKWDKT MDLFVWSVEWILCPMQEKGE KKELFKHVSHRIKETDFLVQ GMGKNVFQKCCEFYRLAGTS SCIEGEDGSETKEERTQILQ KSGLKFYTKTFPYNTTHIMD SKKLVELAIHEKCIGELLKN TTVIEFPTIFVAMTEADLPE GYEVLHQE

Data sets:
Data typeCount
13C chemical shifts824
15N chemical shifts202
1H chemical shifts1355

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 188 residues - 21864.262 Da.

1   GLYPROHISMETARGASPSERTHRGLUCYS
2   GLNARGILEILEARGARGGLYVALASNCYS
3   LEUMETLEUPROLYSGLYMETGLNARGSER
4   SERGLNASNARGSERLYSTRPASPLYSTHR
5   METASPLEUPHEVALTRPSERVALGLUTRP
6   ILELEUCYSPROMETGLNGLULYSGLYGLU
7   LYSLYSGLULEUPHELYSHISVALSERHIS
8   ARGILELYSGLUTHRASPPHELEUVALGLN
9   GLYMETGLYLYSASNVALPHEGLNLYSCYS
10   CYSGLUPHETYRARGLEUALAGLYTHRSER
11   SERCYSILEGLUGLYGLUASPGLYSERGLU
12   THRLYSGLUGLUARGTHRGLNILELEUGLN
13   LYSSERGLYLEULYSPHETYRTHRLYSTHR
14   PHEPROTYRASNTHRTHRHISILEMETASP
15   SERLYSLYSLEUVALGLULEUALAILEHIS
16   GLULYSCYSILEGLYGLULEULEULYSASN
17   THRTHRVALILEGLUPHEPROTHRILEPHE
18   VALALAMETTHRGLUALAASPLEUPROGLU
19   GLYTYRGLUVALLEUHISGLNGLU

Samples:

sample_1: Box C/D snoRNA protein 1, [U-13C; U-15N], 1 mM; sodium chloride 150 mM; sodium phosphate 10 mM; TCEP 0.5 mM

sample_2: Box C/D snoRNA protein 1, [U-13C; U-15N; U-2H], 1 mM; sodium chloride 150 mM; sodium phosphate 10 mM; TCEP 0.5 mM

sample_3: Box C/D snoRNA protein 1, [U-15N], 1 mM; sodium chloride 150 mM; sodium phosphate 10 mM; TCEP 0.5 mM; Pf1 phage 12 mg/mL

sample_conditions_1: ionic strength: 150 mM; pH: 6.4; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D CCCONHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCACOsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - structure calculation

TOPSPIN, Bruker Biospin - collection, processing

NMR spectrometers:

  • Bruker AvanceIII 600 MHz
  • Bruker AvanceIII 950 MHz

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