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BMRB Entry 36261 BMRB - Biological Magnetic Resonance Bank

BMRB Entry 36261

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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/BMR36261
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
Solution structure of the chromodomain of yeast Eaf3
Deposition date:
2019-05-31
Original release date:
2025-09-27
Authors:
Okuda, M.; Nishimura, Y.
Citation:

Citation: Okuda, Masahiko; Nishimura, Yoshifumi. "The Eaf3 chromodomain acts as a pH sensor for gene expression by altering its binding affinity for histone methylated-lysine residues."  Biosci. Rep. 40, .-. (2020).
PubMed: 32031206

Assembly members:

Assembly members:
Chromatin modification-related protein EAF3, polymer, 123 residues, 14103.013 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Chromatin modification-related protein EAF3: GSHMVDLEQEFALGGRCLAF HGPLMYEAKILKIWDPSSKM YTSIPNDKPGGSSQATKEIK PQKLGEDESIPEEIINGKCF FIHYQGWKSSWDEWVGYDRI RAYNEENIAMKKRLANEAKE AKK

Data sets:
Data typeCount
13C chemical shifts510
15N chemical shifts124
1H chemical shifts740

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 123 residues - 14103.013 Da.

1   GLYSERHISMETVALASPLEUGLUGLNGLU
2   PHEALALEUGLYGLYARGCYSLEUALAPHE
3   HISGLYPROLEUMETTYRGLUALALYSILE
4   LEULYSILETRPASPPROSERSERLYSMET
5   TYRTHRSERILEPROASNASPLYSPROGLY
6   GLYSERSERGLNALATHRLYSGLUILELYS
7   PROGLNLYSLEUGLYGLUASPGLUSERILE
8   PROGLUGLUILEILEASNGLYLYSCYSPHE
9   PHEILEHISTYRGLNGLYTRPLYSSERSER
10   TRPASPGLUTRPVALGLYTYRASPARGILE
11   ARGALATYRASNGLUGLUASNILEALAMET
12   LYSLYSARGLEUALAASNGLUALALYSGLU
13   ALALYSLYS

Samples:

13C_15N_H2O: Eaf3, [U-13C; U-15N], 1.47 mM; dithiothreitol 5 mM; sodium chloride 20 mM; potassium phosphate 10 mM; H2O 90%; D2O, [U-2H], 10%

13C_15N_D2O: Eaf3, [U-13C; U-15N], 1.47 mM; dithiothreitol 5 mM; sodium chloride 20 mM; potassium phosphate 10 mM; D2O, [U-2H], 100%

15N: Eaf3, [U-15N], 1.47 mM; dithiothreitol 5 mM; sodium chloride 20 mM; potassium phosphate 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 30 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC13C_15N_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC13C_15N_D2Oisotropicsample_conditions_1
3D CBCANH13C_15N_H2Oisotropicsample_conditions_1
3D CBCA(CO)NH13C_15N_H2Oisotropicsample_conditions_1
3D HNCA13C_15N_H2Oisotropicsample_conditions_1
3D HCCH-TOCSY13C_15N_D2Oisotropicsample_conditions_1
3D H(CC)(CO)HN13C_15N_H2Oisotropicsample_conditions_1
3D CC(CO)NH13C_15N_H2Oisotropicsample_conditions_1
3D HBHA(CO)NH13C_15N_H2Oisotropicsample_conditions_1
3D HNCO13C_15N_H2Oisotropicsample_conditions_1
3D HN(CA)CO13C_15N_H2Oisotropicsample_conditions_1
3D HN(CO)CA13C_15N_H2Oisotropicsample_conditions_1
3D HNHA13C_15N_H2Oisotropicsample_conditions_1
3D HNCG13C_15N_H2Oisotropicsample_conditions_1
3D HN(CO)HB13C_15N_H2Oisotropicsample_conditions_1
3D HNHB13C_15N_H2Oisotropicsample_conditions_1
3D HN(CO)CG13C_15N_H2Oisotropicsample_conditions_1
2D HBCBCGCEHE13C_15N_D2Oisotropicsample_conditions_1
2D CGCBH13C_15N_D2Oisotropicsample_conditions_1
2D HBCBCDHD13C_15N_D2Oisotropicsample_conditions_1
2D CGCEH13C_15N_D2Oisotropicsample_conditions_1
3D HCCH-COSY13C_15N_D2Oisotropicsample_conditions_1
2D CGCDH13C_15N_D2Oisotropicsample_conditions_1
2D 1H-1H TOCSY13C_15N_D2Oisotropicsample_conditions_1
2D DQF-COSY13C_15N_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY13C_15N_D2Oisotropicsample_conditions_1
3D 1H-15N NOESY13C_15N_H2Oisotropicsample_conditions_1

Software:

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

NMRView, Johnson, One Moon Scientific - peak picking

NMRView, Johnson, One Moon Scientific - chemical shift assignment

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

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

MOLMOL, Koradi, Billeter and Wuthrich - data analysis

PROCHECK / PROCHECK-NMR, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton - data analysis

NMR spectrometers:

  • Bruker AVANCE 500 MHz
  • Bruker AVANCE 600 MHz
  • Bruker AVANCE 800 MHz

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