BMRB Entry 11115

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR11115
MolProbity Validation Chart

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Title:
Complex structure of the zf-CW domain and the H3K4me3 peptide
Deposition date:
2010-03-24
Original release date:
2010-10-01
Authors:
He, Fahu; Muto, Yutaka; Inoue, Makoto; Kigawa, Takanori; Shirouzu, Mikako; Terada, Takaho; Yokoyama, Shigeyuki
Citation:

Citation: He, Fahu; Umehara, Takashi; Saito, Kohei; Harada, Takushi; Watanabe, Satoru; Yabuki, Takashi; Kigawa, Takanori; Takahashi, Mari; Kuwasako, Kanako; Tsuda, Kengo; Matsuda, Takayoshi; Aoki, Masaaki; Seki, Eiko; Kobayashi, Naohiro; Guntert, Peter; Yokoyama, Shigeyuki; Muto, Yutaka. "Structural insight into the zinc finger CW domain as a histone modification reader"  Structure 18, 1127-1139 (2010).
PubMed: 20826339

Assembly members:

Assembly members:
zf-CW domain, polymer, 69 residues, 7648.395 Da.
H3K4me3 peptide, polymer, 10 residues, 1192.423 Da.
ZN, non-polymer, 65.409 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: E. coli - cell free   Vector: P060116-12

Entity Sequences (FASTA):

Entity Sequences (FASTA):
zf-CW domain: GSSGSSGEISGFGQCLVWVQ CSFPNCGKWRRLCGNIDPSV LPDNWSCDQNTDVQYNRCDI PEETWTGLE
H3K4me3 peptide: ARTXQTARKS

Data sets:
Data typeCount
13C chemical shifts272
15N chemical shifts75
1H chemical shifts496

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1zf-CW domain1
2H3K4me3 peptide2
3ZINC ION3

Entities:

Entity 1, zf-CW domain 69 residues - 7648.395 Da.

1   GLYSERSERGLYSERSERGLYGLUILESER
2   GLYPHEGLYGLNCYSLEUVALTRPVALGLN
3   CYSSERPHEPROASNCYSGLYLYSTRPARG
4   ARGLEUCYSGLYASNILEASPPROSERVAL
5   LEUPROASPASNTRPSERCYSASPGLNASN
6   THRASPVALGLNTYRASNARGCYSASPILE
7   PROGLUGLUTHRTRPTHRGLYLEUGLU

Entity 2, H3K4me3 peptide 10 residues - 1192.423 Da.

contains N-TRIMETHYLLYSINE, instead of 4K

1   ALAARGTHRM3LGLNTHRALAARGLYSSER

Entity 3, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: zf-CW domain, [U-13C; U-15N], 1.1 mM; H3K4me3 peptide 1.1 mM; ZINC ION 50 uM; D-TRIS-HCL 20 mM; NACL 100 mM; D-DTT 1 mM; NAN3 0.02%; ZNCL2 50 uM; IDA 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1

Software:

NMRPipe v5.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

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

AMBER v9.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMRView v5.0, Johnson, One Moon Scientific - data analysis

xwinnmr v3.0, Bruker Biospin - collection

Kujira v0.9839, Naohiro Kobayashi - data analysis

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker DRX 600 MHz

Related Database Links:

BMRB 11358 11359 11360 11361 11362
PDB
DBJ BAA91424 BAC04028 BAG62414 BAG63489
EMBL CAB66669
GB AAH02725 AIC60275 EAW76538 EAW76539 EAW76540
REF NP_001244937 NP_060454 XP_002803268 XP_003318693 XP_003318694
SP Q9H0M4
AlphaFold Q9H0M4 Q93081

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