BMRB Entry 19425

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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/BMR19425
MolProbity Validation Chart

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Title:
X-ray crystallography-solution NMR hybrid structure of mouse RyR2 domain A.
Deposition date:
2013-08-13
Original release date:
2013-09-10
Authors:
Amador, Fernando; Stathopulos, Peter; Seabrook, Genevieve; Ikura, Mitsuhiko
Citation:

Citation: Amador, Fernando; Kimlicka, Lynn; Stathopulos, Peter; Gasmi-Seabrook, Genevieve; Maclennan, David; Van Petegem, Filip; Ikura, Mitsuhiko. "Type 2 Ryanodine Receptor Domain A Contains a Unique and Dynamic -Helix That Transitions to a -Strand in a Mutant Linked with a Heritable Cardiomyopathy."  J. Mol. Biol. 425, 4034-4046 (2013).
PubMed: 23978697

Assembly members:

Assembly members:
entity, polymer, 219 residues, 23049.213 Da.

Natural source:

Natural source:   Common Name: Mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-32a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSGSEIQFLRTDDEVVLQCT ATIHKEQQKLCLAAEGFGNR LCFLESTSNSKNVPPDLSIC TFVLEQSLSVRALQEMLANT VEKSEGQVDVEKWKFMMKTA QGGGHRTLLYGHAILLRHSY SGMYLCCLSTSRSSTDKLAF DVGLQEDTTGEACWWTIHPA SKQRSEGEKVRVGDDLILVS VSSERYLHLSYGNSSWHVDA AFQQTLWSVAPISSGSEAA

Data sets:
Data typeCount
13C chemical shifts541
15N chemical shifts185
1H chemical shifts185

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1mouse RyR2 domain A1

Entities:

Entity 1, mouse RyR2 domain A 219 residues - 23049.213 Da.

Residues 1-4 are a cloning artifact; residues 5-219 correspond to 10-224 of mouse RyR2 (E9Q401).

1   GLYSERGLYSERGLUILEGLNPHELEUARG
2   THRASPASPGLUVALVALLEUGLNCYSTHR
3   ALATHRILEHISLYSGLUGLNGLNLYSLEU
4   CYSLEUALAALAGLUGLYPHEGLYASNARG
5   LEUCYSPHELEUGLUSERTHRSERASNSER
6   LYSASNVALPROPROASPLEUSERILECYS
7   THRPHEVALLEUGLUGLNSERLEUSERVAL
8   ARGALALEUGLNGLUMETLEUALAASNTHR
9   VALGLULYSSERGLUGLYGLNVALASPVAL
10   GLULYSTRPLYSPHEMETMETLYSTHRALA
11   GLNGLYGLYGLYHISARGTHRLEULEUTYR
12   GLYHISALAILELEULEUARGHISSERTYR
13   SERGLYMETTYRLEUCYSCYSLEUSERTHR
14   SERARGSERSERTHRASPLYSLEUALAPHE
15   ASPVALGLYLEUGLNGLUASPTHRTHRGLY
16   GLUALACYSTRPTRPTHRILEHISPROALA
17   SERLYSGLNARGSERGLUGLYGLULYSVAL
18   ARGVALGLYASPASPLEUILELEUVALSER
19   VALSERSERGLUARGTYRLEUHISLEUSER
20   TYRGLYASNSERSERTRPHISVALASPALA
21   ALAPHEGLNGLNTHRLEUTRPSERVALALA
22   PROILESERSERGLYSERGLUALAALA

Samples:

sample_1: entity, [U-13C; U-15N; U-2H], 0.4 mM; sodium phosphate 20 mM; sodium chloride 300 mM; TCEP 2 mM; DTT 5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.328 M; pH: 7; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - chemical shift calculation, data analysis, geometry optimization

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

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

UNP E9Q401
PDB
EMBL CAA66975 CAC18855
GB AAA31179 AAA93465 AAG34081 AAI67757 AAI72794
PRF 1617118A
REF NP_001026 NP_001076226 NP_076357 XP_002808310 XP_002923703
SP E9Q401 P30957 Q92736
AlphaFold Q9ERN6 E9Q401 P30957 Q92736

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