BMRB Entry 16778

Title:
Solution structure of the CBX7 chromodomain in complex with a H3K27me2 peptide
Deposition date:
2010-03-17
Original release date:
2011-05-26
Authors:
Yap, Kyoko; Zeng, Lei; Zhou, Ming-Ming
Citation:

Citation: Yap, Kyoko; Li, Side; Munoz-Cabello, Ana; Raguz, Selina; Zeng, Lei; Mujtaba, Shiraz; Gil, Jesus; Walsh, Martin; Zhou, Ming-Ming. "Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a"  Mol. Cell 38, 662-674 (2010).
PubMed: 20541999

Assembly members:

Assembly members:
CBX7_chromodomain, polymer, 71 residues, 8555.949 Da.
H3K27me2_peptide, polymer, 16 residues, 1726.093 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CBX7_chromodomain: MELSAIGEQVFAVESIRKKR VRKGKVEYLVKWKGWPPKYS TWEPEEHILDPRLVMAYEEK EERDRASGYRK
H3K27me2_peptide: APRKQLATKAARXSAP

Data sets:
Data typeCount
13C chemical shifts308
15N chemical shifts68
1H chemical shifts631

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CBX7_chromodomain1
2H3K27me2_peptide2

Entities:

Entity 1, CBX7_chromodomain 71 residues - 8555.949 Da.

1   METGLULEUSERALAILEGLYGLUGLNVAL
2   PHEALAVALGLUSERILEARGLYSLYSARG
3   VALARGLYSGLYLYSVALGLUTYRLEUVAL
4   LYSTRPLYSGLYTRPPROPROLYSTYRSER
5   THRTRPGLUPROGLUGLUHISILELEUASP
6   PROARGLEUVALMETALATYRGLUGLULYS
7   GLUGLUARGASPARGALASERGLYTYRARG
8   LYS

Entity 2, H3K27me2_peptide 16 residues - 1726.093 Da.

1   ALAPROARGLYSGLNLEUALATHRLYSALA
2   ALAARGMLYSERALAPRO

Samples:

sample_1: CBX7 chromodomain, [U-100% 15N], 0.5 mM; H3K27me2 peptide 0.75 mM; sodium phosphate 4.3 mM; potassium phosphate 1.4 mM; DTT 5 mM; sodium chloride 137 mM; potassium chloride 3 mM; H2O 90%; D2O 10%

sample_2: CBX7 chromodomain, [U-100% 13C; U-100% 15N], 0.5 mM; H3K27me2 peptide 0.75 mM; sodium phosphate 4.3 mM; potassium phosphate 1.4 mM; DTT 5 mM; sodium chloride 137 mM; potassium chloride 3 mM; H2O 90%; D2O 10%

sample_3: H3K27me2 peptide 0.5 mM; sodium phosphate 4.3 mM; potassium phosphate 1.4 mM; DTT 5 mM; sodium chloride 137 mM; potassium chloride 3 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 140 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_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(COCA)CBsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1

Software:

ARIA v2.0, Linge, O'Donoghue and Nilges - chemical shift assignment, structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

TALOS, Cornilescu, Delaglio and Bax - data analysis

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker Avance 800 MHz
  • Bruker DRX 600 MHz

Related Database Links:

BMRB 15674 17072 17079 6997
PDB
DBJ BAI46775 BAM62356
GB AAH21398 AAH51773 AAH62392 AAR26721 AAX94038 AAY18719 ABB83163 ABL95239 ABL95241 ABN80289
REF NP_001179547 NP_001247702 NP_659060 NP_783640 NP_954548
SP O95931 P60889 Q8VDS3
TPG DAA29144
AlphaFold Q8VDS3 O95931 P60889

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