BMRB Entry 17569

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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/BMR17569
MolProbity Validation Chart

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Title:
Solution structure of the ADD domain of ATRX complexed with histone tail H3 1-15 K9me3
Deposition date:
2011-04-08
Original release date:
2011-06-16
Authors:
Eustermann, Sebastian; Yang, Ji-Chun; Neuhaus, David
Citation:

Citation: Eustermann, Sebastian; Yang, Ji-Chun; Law, Martin; Amos, Rachel; Chapman, Lynda; Jelinska, Clare; Garrick, David; Clynes, David; Gibbons, Richard; Rhodes, Daniela; Higgs, Douglas; Neuhaus, David. "Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin."  Nat. Struct. Mol. Biol. 18, 777-782 (2011).
PubMed: 21666677

Assembly members:

Assembly members:
ATRX_ADD_domain, polymer, 142 residues, 16274.673 Da.
H3_tail_1-15_K9me3, polymer, 15 residues, 1607.892 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: Escherichia coli   Vector: pET30a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ATRX_ADD_domain: GAMADKRGDGLHGIVSCTAC GQQVNHFQKDSIYRHPSLQV LICKNCFKYYMSDDISRDSD GMDEQCRWCAEGGNLICCDF CHNAFCKKCILRNLGRKELS TIMDENNQWYCYICHPEPLL DLVTACNSVFENLEQLLQQN KK
H3_tail_1-15_K9me3: ARTKQTARXSTGGKA

Data sets:
Data typeCount
13C chemical shifts393
15N chemical shifts148
1H chemical shifts949

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1ATRX_ADD_domain1
2H3_tail_1-15_K9me32
3ZN1_13
4ZN1_23
5ZN1_33

Entities:

Entity 1, ATRX_ADD_domain 142 residues - 16274.673 Da.

1   GLYALAMETALAASPLYSARGGLYASPGLY
2   LEUHISGLYILEVALSERCYSTHRALACYS
3   GLYGLNGLNVALASNHISPHEGLNLYSASP
4   SERILETYRARGHISPROSERLEUGLNVAL
5   LEUILECYSLYSASNCYSPHELYSTYRTYR
6   METSERASPASPILESERARGASPSERASP
7   GLYMETASPGLUGLNCYSARGTRPCYSALA
8   GLUGLYGLYASNLEUILECYSCYSASPPHE
9   CYSHISASNALAPHECYSLYSLYSCYSILE
10   LEUARGASNLEUGLYARGLYSGLULEUSER
11   THRILEMETASPGLUASNASNGLNTRPTYR
12   CYSTYRILECYSHISPROGLUPROLEULEU
13   ASPLEUVALTHRALACYSASNSERVALPHE
14   GLUASNLEUGLUGLNLEULEUGLNGLNASN
15   LYSLYS

Entity 2, H3_tail_1-15_K9me3 15 residues - 1607.892 Da.

1   ALAARGTHRLYSGLNTHRALAARGM3LSER
2   THRGLYGLYLYSALA

Entity 3, ZN1_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: ATRX ADD domain, [U-98% 13C; U-98% 15N], 200 uM; H3 tail 1-15 K9me3 200 uM; TRIS, [U-99% 2H], 50 mM; sodium chloride 200 mM; zinc sulfate 150 uM; DTT, [U-99% 2H], 1 mM; H2O 95%; D2O 5%

sample_2: ATRX ADD domain, [U-98% 13C; U-98% 15N], 200 uM; H3 tail 1-15 K9me3 200 uM; TRIS, [U-99% 2H], 50 mM; sodium chloride 200 mM; zinc sulfate 150 uM; DTT, [U-99% 2H], 1 mM; D2O 100%

sample_conditions_1: ionic strength: 250 mM; pH: 7.0; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphatic (constant-time)sample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromatic (constant-time)sample_1isotropicsample_conditions_1
2D 1H-1H NOESY (13C-H rejected in F1 and F2)sample_2isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H[C]CH-TOCSYsample_1isotropicsample_conditions_1
3D [H]CCH-TOCSYsample_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
2D 1H-1H TOCSY (13C-H rejected in F1 and F2)sample_2isotropicsample_conditions_1
2D 1H-1H NOESY (15N-H rejected in F2)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic (rejected 13C-H in F1, 12C-H in F3)sample_2isotropicsample_conditions_1
2D 1H-1H NOESY (13C-H rejected F1, 12C-H rejected F2)sample_2isotropicsample_conditions_1
2D 1H-1H NOESY (13C-H and 15N-H rejected in F1 and F2)sample_1isotropicsample_conditions_1

Software:

X-PLOR NIH v2.19, Schwieters, Kuszewski, Tjandra and Clore - structure solution

SPARKY, Goddard - chemical shift assignment

TOPSPIN v2.1, Bruker Biospin - processing

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker DMX 600 MHz
  • Bruker DRX 500 MHz

Related Database Links:

BMRB 15001
PDB
DBJ BAC28096 BAC40142 BAC81110 BAC81111 BAC81112
EMBL CAB90351 CAI40710 CAI42674 CAI42675 CAI43115
GB AAB40698 AAB40699 AAB40700 AAB49969 AAB49970
REF NP_000480 NP_001009018 NP_033556 NP_612114 XP_001099671
SP P46100 Q61687 Q7YQM3 Q7YQM4
TPG DAA12976 DAA12977
AlphaFold P46100 Q61687 Q7YQM3 Q7YQM4 Q93081

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