BMRB Entry 19914

Title:
NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa)
Deposition date:
2014-04-16
Original release date:
2014-08-04
Authors:
Zhang, Yan; Yang, Huirong; Guo, Xue; Rong, Naiyan; Song, Yujiao; Xu, Youwei; Lan, Wenxian; Xu, Yanhui; Cao, Chunyang
Citation:

Citation: Zhang, Yan; Yang, Huirong; Guo, Xue; Rong, Naiyan; Rong, Yujiao; Xu, Youwei; Lan, Wenxian; Xu, Yanhui; Cao, Chunyang. "The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B"  Protein Cell ., .-. (2014).
PubMed: 24952722

Assembly members:

Assembly members:
entity_1, polymer, 55 residues, 7360.083 Da.
ZINC ION, non-polymer, 65.409 Da.
entity_3, polymer, 10 residues, Formula weight is not available

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: pGEX-6p-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AVDLYVCLLCGSGNDEDRLL LCDGCDDSYHTFCLIPPLHD VPKGDWRCPKCLAQE
entity_3: ARTKQTARKS

Data sets:
Data typeCount
13C chemical shifts165
15N chemical shifts51
1H chemical shifts396

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2ZINC ION_12
3ZINC ION_22
4H3K4me0(1-10aa)3

Entities:

Entity 1, entity_1 55 residues - 7360.083 Da.

1   ALAVALASPLEUTYRVALCYSLEULEUCYS
2   GLYSERGLYASNASPGLUASPARGLEULEU
3   LEUCYSASPGLYCYSASPASPSERTYRHIS
4   THRPHECYSLEUILEPROPROLEUHISASP
5   VALPROLYSGLYASPTRPARGCYSPROLYS
6   CYSLEUALAGLNGLU

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Entity 3, H3K4me0(1-10aa) 10 residues - Formula weight is not available

1   ALAARGTHRLYSGLNTHRALAARGLYSSER

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.8 – 2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 7.4; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C 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 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

BMRB 19913
PDB
DBJ BAC30898 BAD90482 BAE37363 BAE89761 BAG53706
EMBL CAB43532 CAB61368 CAB63108 CAH65222
GB AAD16061 AAH48180 AAH57318 AAI56050 AAI57032
REF NP_001026200 NP_001100647 NP_001300971 NP_006609 NP_690855
SP Q5F3R2 Q80Y84 Q9UGL1
TPG DAA21261
AlphaFold Q9UGL1 Q5F3R2 Q80Y84

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