BMRB Entry 16210

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16210
MolProbity Validation Chart

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Title:
Solution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3
Deposition date:
2009-03-12
Original release date:
2009-05-29
Authors:
Song, Jikui; Wang, Zhanxin; Patel, Dinshaw
Citation:

Citation: Wang, Gang; Song, Jikui; Wang, Zhanxin; Dormann, Holger; Casadio, Fabio; Li, Haitao; Luo, Jun-Li; Patel, Dinshaw; Allis, C.. "Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger"  Nature 459, 847-851 (2009).
PubMed: 19430464

Assembly members:

Assembly members:
JARID1A_PHD_finger_3, polymer, 52 residues, 5802.505 Da.
ZN, non-polymer, 65.409 Da.
H3(1-9)K4me3, polymer, 52 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: pRSFDuet-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
JARID1A_PHD_finger_3: SVCAAQNCQRPCKDKVDWVQ CDGGCDEWFHQVCVGVSPEM AENEDYICINCA
H3(1-9)K4me3: ARTXQTARK

Data sets:
Data typeCount
13C chemical shifts203
15N chemical shifts58
1H chemical shifts363

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1JARID1A PHD finger 31
2ZINC ION_12
3ZINC ION_22
4H3K4(1-9)me33

Entities:

Entity 1, JARID1A PHD finger 3 52 residues - 5802.505 Da.

1   SERVALCYSALAALAGLNASNCYSGLNARG
2   PROCYSLYSASPLYSVALASPTRPVALGLN
3   CYSASPGLYGLYCYSASPGLUTRPPHEHIS
4   GLNVALCYSVALGLYVALSERPROGLUMET
5   ALAGLUASNGLUASPTYRILECYSILEASN
6   CYSALA

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Entity 3, H3K4(1-9)me3 52 residues - Formula weight is not available

1   ALAARGTHRM3LGLNTHRALAARGLYS

Samples:

sample_1: JARID1A PHD finger 3, [U-100% 13C; U-100% 15N], 0.2 – 0.5 mM; H3(1-9)K4Me30.2 – 0.5 mM; DTT 0.5 mM; ZINC ION 1 mM; sodium phosphate 20 mM

sample_2: JARID1A PHD finger 3, [U-100% 15N], 0.2 – 0.5 mM; H3(1-9)K4Me30.2 – 0.5 mM; DTT 5 mM; ZINC ION 1 mM; MOPS 10 mM; bacteriophage Pf1 12 mg/ml

sample_conditions_1: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 293.2 K

sample_conditions_2: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 298.2 K

Experiments:

NameSampleSample stateSample conditions
1H,15N-HSQCsample_1isotropicsample_conditions_1
1H,13C-HSQCsample_1isotropicsample_conditions_1
HNCACBsample_1isotropicsample_conditions_1
HBHACONHsample_1isotropicsample_conditions_1
CBCACONHsample_1isotropicsample_conditions_1
2D 1H, 1H-NOESYsample_1isotropicsample_conditions_1
HCCHTOCSYsample_1isotropicsample_conditions_1
15N-EDITED 1H,1H-NOESYsample_1isotropicsample_conditions_1
13C-EDITED 1H,1H-NOESYsample_1isotropicsample_conditions_1
15N IPAP HSQCsample_1isotropicsample_conditions_2
13C,15N-FILTERED, 13C-EDITED 1H,1H-NOESYsample_1isotropicsample_conditions_1
13C,15N-FILTERED, 2D 1H,1H-NOESYsample_1isotropicsample_conditions_1
15N IPAP HSQCsample_2anisotropicsample_conditions_2

Software:

X-PLOR NIH v2.18, Schwieters, Kuszewski, Tjandra and Clore - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker DMX 800 MHz

Related Database Links:

BMRB 16209
PDB
DBJ BAE06081 BAG10524
GB ACH71258 ELK02599 ELK24529 ELV13200 EOB07246
REF NP_001036068 NP_001264106 XP_001373115 XP_001914992 XP_002712829
SP P29375
AlphaFold P29375

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