BMRB Entry 11496

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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/BMR11496
MolProbity Validation Chart

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Title:
Solution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide
Deposition date:
2012-04-18
Original release date:
2012-08-27
Authors:
Shimojo, Hideaki; Nishimura, Yoshifumi
Citation:

Citation: Ishida, Mayumi; Shimojo, Hideaki; Hayashi, Aki; Kawaguchi, Rika; Ohtani, Yasuko; Uegaki, Koichi; Nishimura, Yoshifumi; Nakayama, Jun-ichi. "Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing"  Mol. Cell 47, 228-241 (2012).
PubMed: 22727667

Assembly members:

Assembly members:
Chp1_chromodomain, polymer, 75 residues, 8909.997 Da.
Histone_H3K9me3, polymer, 18 residues, 2025.379 Da.

Natural source:

Natural source:   Common Name: fission yeast   Taxonomy ID: 4896   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Schizosaccharomyces pombe

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Chp1_chromodomain: MVSVKPLPDIDSNEGETDAD VYEVEDILADRVNKNGINEY YIKWAGYDWYDNTWEPEQNL FGAEKVLKKWKKRKK
Histone_H3K9me3: ARTKQTARXSTGGKAPRY

Data sets:
Data typeCount
13C chemical shifts352
15N chemical shifts82
1H chemical shifts599

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 75 residues - 8909.997 Da.

1   METVALSERVALLYSPROLEUPROASPILE
2   ASPSERASNGLUGLYGLUTHRASPALAASP
3   VALTYRGLUVALGLUASPILELEUALAASP
4   ARGVALASNLYSASNGLYILEASNGLUTYR
5   TYRILELYSTRPALAGLYTYRASPTRPTYR
6   ASPASNTHRTRPGLUPROGLUGLNASNLEU
7   PHEGLYALAGLULYSVALLEULYSLYSTRP
8   LYSLYSARGLYSLYS

Entity 2, entity_2 18 residues - 2025.379 Da.

ARTKQTAR(M3L)STGGKAPRY

1   ALAARGTHRLYSGLNTHRALAARGM3LSER
2   THRGLYGLYLYSALAPROARGTYR

Samples:

sample_1: Chp1_chromodomain, [U-99% 13C; U-99% 15N], 0.3 – 0.5 mM; Histone_H3K9me30.3 – 0.5 mM; potassium phosphate 20 mM; sodium chloride 10 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 298 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 HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 13C/15N filtered NOESYsample_1isotropicsample_conditions_1
2D 13C/15N fllterd NOESYsample_1isotropicsample_conditions_1
2D 13C/15N filterd TOCSYsample_1isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

Olivia, Yokochi, Sekiguchi and Inagaki - chemical shift assignment, data analysis, peak picking

ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution

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

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
EMBL CAA92382
REF NP_593666
SP Q10103
GB AAY98280
AlphaFold Q10103

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