BMRB Entry 17071

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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/BMR17071
MolProbity Validation Chart

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Title:
Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide
Deposition date:
2010-07-22
Original release date:
2010-08-18
Authors:
Kaustov, Lilia; Lemak, Alexander; Fares, Christophe; Gutmanas, Aleksandras; Quang, Hui; Loppnau, Peter; Min, Jinrong; Edwards, Al; Arrowsmith, Cheryl
Citation:

Citation: Kaustov, Lilia; Ouyang, Hui; Amaya, Maria; Lemak, Alexander; Nady, Nataliya; Duan, Shili; Wasney, Gregory; Li, Zhihong; Vedadi, Masoud; Schapira, Matthieu; Min, Jinrong; Arrowsmith, Cheryl. "Recognition and specificity determinants of the human cbx chromodomains."  J. Biol. Chem. 286, 521-529 (2011).
PubMed: 21047797

Assembly members:

Assembly members:
Cbx3, polymer, 54 residues, 6354.158 Da.
H3K9me3, polymer, 15 residues, 1607.892 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28a-mhl

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Cbx3: GEFVVEKVLDRRVVNGKVEY FLKWKGFTDADNTWEPEENL DCPELIEAFLNSQK
H3K9me3: ARTKQTARXSTGGKA

Data typeCount
13C chemical shifts241
15N chemical shifts56
1H chemical shifts424

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Cbx31
2H3K9me32

Entities:

Entity 1, Cbx3 54 residues - 6354.158 Da.

1   GLYGLUPHEVALVALGLULYSVALLEUASP
2   ARGARGVALVALASNGLYLYSVALGLUTYR
3   PHELEULYSTRPLYSGLYPHETHRASPALA
4   ASPASNTHRTRPGLUPROGLUGLUASNLEU
5   ASPCYSPROGLULEUILEGLUALAPHELEU
6   ASNSERGLNLYS

Entity 2, H3K9me3 15 residues - 1607.892 Da.

X = N-TRIMETHYLLYSINE

1   ALAARGTHRLYSGLNTHRALAARGM3LSER
2   THRGLYGLYLYSALA

Samples:

sample_1: Cbx3, [U-13C; U-15N], 0.43 mM; H3K9me3 1.2 mM; sodium phosphate 20 mM; sodium chloride 200 mM; DTT 2 mM; TCEP 1 mM; PMSF 0.5 mM; Benzamidine 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D-15N-NOESYsample_1isotropicsample_conditions_1
3D-13C-NOESYsample_1isotropicsample_conditions_1
3D -13C-aromatic-NOESYsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_1isotropicsample_conditions_1
13C/15N-filtered/edited NOESYsample_1isotropicsample_conditions_1
3D aro 1H-13C NOESYsample_1isotropicsample_conditions_1
3D-aromatic 1H-13C-TOCSYsample_1isotropicsample_conditions_1

Software:

ABACUS, Grishaev - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

SPARKY, Goddard - peak picking

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

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Varian INOVA 500 MHz

Related Database Links:

PDB
DBJ BAA33401 BAA83340 BAB22450 BAC39078 BAE27125
EMBL CAA40012 CAC42944 CAH92483
GB AAB48101 AAF62370 AAH00954 AAH18354 AAH59831
REF NP_001008314 NP_001094668 NP_001126464 NP_001180536 NP_001233631
SP P23198 Q13185 Q5R6X7
TPG DAA30517
AlphaFold P23198 Q13185 Q5R6X7 P17320

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