BMRB Entry 17138

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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/BMR17138
MolProbity Validation Chart

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Title:
Solution structure of the coiled-coil complex between MBD2 and p66alpha
Deposition date:
2010-08-20
Original release date:
2012-08-02
Authors:
Williams, David; Scarsdale, Joe
Citation:

Citation: Gnanapragasam, Merlin; Scarsdale, Joe; Amaya, Maria; Webb, Heather; Walavalkar, Ninad; Ginder, Gordon; David, Williams. "Solution structure and functional analyses of a coiled-coil interaction between MBD2 and p66alpha integral to the formation of the MeCP1 nucleosome remodeling complex"  .

Assembly members:

Assembly members:
p66-alpha, polymer, 43 residues, 5116.060 Da.
MBD2, polymer, 36 residues, 4181.826 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: pET32a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
p66-alpha: GSPEERERMIKQLKEELRLE EAKLVLLKKLRQSQIQKEAT AQK
MBD2: GSKAFIVTDEDIRKQEERVQ QVRKKLEEALMADILS

Data sets:
Data typeCount
13C chemical shifts357
15N chemical shifts74
1H chemical shifts588

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1p66-alpha1
2MBD22

Entities:

Entity 1, p66-alpha 43 residues - 5116.060 Da.

N-terminal Gly-Ser residues represent non-native sequence from an affinity tag.

1   GLYSERPROGLUGLUARGGLUARGMETILE
2   LYSGLNLEULYSGLUGLULEUARGLEUGLU
3   GLUALALYSLEUVALLEULEULYSLYSLEU
4   ARGGLNSERGLNILEGLNLYSGLUALATHR
5   ALAGLNLYS

Entity 2, MBD2 36 residues - 4181.826 Da.

N-terminal Gly-Ser residues represent non-native sequence from an affinity tag. Numbering reflects the MBD2b isoform.

1   GLYSERLYSALAPHEILEVALTHRASPGLU
2   ASPILEARGLYSGLNGLUGLUARGVALGLN
3   GLNVALARGLYSLYSLEUGLUGLUALALEU
4   METALAASPILELEUSER

Samples:

15N13Cp66a:MBD2: p66-alpha, [U-99% 13C; U-99% 15N], 1.0 mM; MBD2 1.0 mM; H2O 90%; D2O 10%

15N13CMBD2:p66a: MBD2, [U-100% 13C; U-100% 15N], 1.0 mM; p66-alpha 1.0 mM; H2O 90%; D2O 10%

2H15N13Cp66a:2H15N13CMBD2: p66-alpha, [U-100% 13C; U-100% 15N; U-80% 2H], 1.0 mM; MBD2, [U-100% 13C; U-100% 15N; U-80% 2H], 1.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCO15N13Cp66a:MBD2isotropicsample_conditions_1
3D HNCA15N13Cp66a:MBD2isotropicsample_conditions_1
3D HNCACB15N13Cp66a:MBD2isotropicsample_conditions_1
3D HBHA(CO)NH15N13Cp66a:MBD2isotropicsample_conditions_1
3D CBCA(CO)NH15N13Cp66a:MBD2isotropicsample_conditions_1
3D HN(CO)CA15N13Cp66a:MBD2isotropicsample_conditions_1
3D 1H-15N NOESY15N13Cp66a:MBD2isotropicsample_conditions_1
3D 1H-13C NOESY15N13Cp66a:MBD2isotropicsample_conditions_1
3D C(CO)NH15N13Cp66a:MBD2isotropicsample_conditions_1
2D 1H-15N HSQC15N13Cp66a:MBD2isotropicsample_conditions_1
3D HNCO15N13CMBD2:p66aisotropicsample_conditions_1
3D HNCA15N13CMBD2:p66aisotropicsample_conditions_1
3D HNCACB15N13CMBD2:p66aisotropicsample_conditions_1
3D HBHA(CO)NH15N13CMBD2:p66aisotropicsample_conditions_1
3D HN(CO)CA15N13CMBD2:p66aisotropicsample_conditions_1
3D HCCH-TOCSY15N13CMBD2:p66aisotropicsample_conditions_1
3D 1H-15N NOESY15N13CMBD2:p66aisotropicsample_conditions_1
3D 1H-13C NOESY15N13CMBD2:p66aisotropicsample_conditions_1
3D CBCA(CO)NH15N13CMBD2:p66aisotropicsample_conditions_1
3D C(CO)NH15N13CMBD2:p66aisotropicsample_conditions_1
2D 1H-15N HSQC15N13CMBD2:p66aisotropicsample_conditions_1
3D HNCO2H15N13Cp66a:2H15N13CMBD2anisotropicsample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

PIPP, Garrett - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Varian UnityPlus 500 MHz
  • Bruker Avance 700 MHz

Related Database Links:

PDB
DBJ BAC40736 BAE89133 BAG59359 BAG73190
EMBL CAH65456 CAH10725
GB AAH11684 AAH38221 AAH89902 AAO31797 ABZ92025 AAC18050 AAC68871 AAC68872 AAD50372 AAD56597
REF NP_001012570 NP_001013903 NP_001106817 NP_001273379 NP_001287875 NP_001108497 NP_003918 NP_034903 XP_001082249 XP_001362190
SP Q86YP4 Q8CHY6 Q9UBB5 Q9Z2E1
TPG DAA15869
AlphaFold Q86YP4 Q8CHY6 Q9UBB5 Q9Z2E1

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