BMRB Entry 17344

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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/BMR17344
MolProbity Validation Chart

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Title:
Solution structure of CHD4-PHD2 in complex with H3K9me3
Deposition date:
2010-12-02
Original release date:
2011-02-01
Authors:
Mansfield, Robyn; Kwan, Ann; Mackay, Joel
Citation:

Citation: Mansfield, Robyn; Musselman, Catherine; Kwan, Ann; Oliver, Samuel; Garske, Adam; Davrazou, Foteini; Denu, John; Kutateladze, Tatiana; Mackay, Joel. "Plant Homeodomain (PHD) Fingers of CHD4 Are Histone H3-binding Modules with Preference for Unmodified H3K4 and Methylated H3K9."  J. Biol. Chem. 286, 11779-11791 (2011).
PubMed: 21278251

Assembly members:

Assembly members:
CHD4-PHD2, polymer, 61 residues, Formula weight is not available
H3K9me3, polymer, 14 residues, Formula weight is not available
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: Escherichia coli   Vector: pGEX-2TE

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CHD4-PHD2: GPLGSDHHMEFCRVCKDGGE LLCCDTCPSSYHIHCLNPPL PEIPNGEWLCPRCTCPALKG K
H3K9me3: ARTKQTARXSTGGY

Data sets:
Data typeCount
13C chemical shifts248
15N chemical shifts61
1H chemical shifts484

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CHD4-PHD21
2H3K9me32
3ZINC ION_13
4ZINC ION_23

Entities:

Entity 1, CHD4-PHD2 61 residues - Formula weight is not available

Non-native N-terminal GPLGS due to cleavage of expression tag.

1   GLYPROLEUGLYSERASPHISHISMETGLU
2   PHECYSARGVALCYSLYSASPGLYGLYGLU
3   LEULEUCYSCYSASPTHRCYSPROSERSER
4   TYRHISILEHISCYSLEUASNPROPROLEU
5   PROGLUILEPROASNGLYGLUTRPLEUCYS
6   PROARGCYSTHRCYSPROALALEULYSGLY
7   LYS

Entity 2, H3K9me3 14 residues - Formula weight is not available

C-terminal Tyr is not part of native H3 sequence, but added for concentration determination by A280.

1   ALAARGTHRLYSGLNTHRALAARGM3LSER
2   THRGLYGLYTYR

Entity 3, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

unlabeled: CHD4-PHD2 1 mM; H3K9me3 1 mM; DSS 20 uM; DTT 1 mM; sodium chloride 5 mM; sodium phosphate 10 mM; H2O 93%; D2O 7%

15N13C_H2O: CHD4-PHD2, [U-100% 13C; U-100% 15N], 1 mM; H3K9me3 1.1 mM; DSS 20 uM; DTT 1 mM; sodium chloride 5 mM; sodium phosphate 10 mM; H2O 93%; D2O 7%

15N13C_D2O: CHD4-PHD2, [U-100% 13C; U-100% 15N], 1 mM; H3K9me3 1.1 mM; DSS 20 uM; DTT 1 mM; sodium chloride 5 mM; sodium phosphate 10 mM; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 15 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15N13C_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC15N13C_D2Oisotropicsample_conditions_1
2D 1H-1H TOCSYunlabeledisotropicsample_conditions_1
2D 1H-1H COSYunlabeledisotropicsample_conditions_1
3D HNCA15N13C_H2Oisotropicsample_conditions_1
3D CBCA(CO)NH15N13C_H2Oisotropicsample_conditions_1
3D HNHA15N13C_H2Oisotropicsample_conditions_1
3D HBHA(CO)NH15N13C_H2Oisotropicsample_conditions_1
3D HNCO15N13C_H2Oisotropicsample_conditions_1
3D HN(CA)CO15N13C_H2Oisotropicsample_conditions_1
3D HCCH-TOCSY15N13C_D2Oisotropicsample_conditions_1
3D CC(CO)NH TOCSY15N13C_H2Oisotropicsample_conditions_1
2D-His HSQC15N13C_H2Oisotropicsample_conditions_1
(HB)CB(CGCD)HD15N13C_H2Oisotropicsample_conditions_1
(HB)CB(CGCDCE)HE15N13C_H2Oisotropicsample_conditions_1
3D 1H-15N NOESY15N13C_H2Oisotropicsample_conditions_1
3D 1H-15N TOCSY15N13C_H2Oisotropicsample_conditions_1
2D 1H-1H NOESYunlabeledisotropicsample_conditions_1
3D 1H-13C NOESY15N13C_D2Oisotropicsample_conditions_1
15N-13C DHF NOESY15N13C_H2Oisotropicsample_conditions_1
13C-13C DHF NOESY15N13C_D2Oisotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - Intermolecular distance calibration

ARIA, Linge, O'Donoghue and Nilges - structure solution

ProcheckNMR, Laskowski and MacArthur - refinement and validation

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ BAE32198
REF XP_012406166 XP_013226542
SWS P68431

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