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Biological Magnetic Resonance Data Bank


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BMRB Entry 18559

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18559
MolProbity Validation Chart

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Title: Solution NMR structure of the PHD domain of human MLL5. Northeast structural genomics consortium target HR6512A.   PubMed: 24130829

Deposition date: 2012-06-29 Original release date: 2012-07-31

Authors: Lemak, Alexander; Yee, Adelinda; Houliston, Scott; Garcia, Maite; Wu, Hong; Min, Jinrong; Arrowsmith, Cheryl

Citation: Lemak, Alexander; Yee, Adelinda; Wu, Hong; Yap, Damian; Zeng, Hong; Dombrovski, Ludmila; Houliston, Scott; Aparicio, Samuel; Arrowsmith, Cheryl. "Solution NMR structure and histone binding of the PHD domain of human MLL5."  PLoS ONE 8, e77020-e77020 (2013).

Assembly members:
MLL5, polymer, 98 residues, 9318.508 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:   Common Name: Humans   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
MLL5: MHHHHHHSSGRENLYFQGSE DGSYGTDVTRCICGFTHDDG YMICCDKCSVWQHIDCMGID RQHIPDTYLCERCQPRNLDK ERAVLLQRRKRENMSDGD

Data sets:
Data typeCount
13C chemical shifts298
15N chemical shifts74
1H chemical shifts472

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1MLL51
2ZINC ION_12
3ZINC ION_22

Entities:

Entity 1, MLL5 98 residues - 9318.508 Da.

1   METHISHISHISHISHISHISSERSERGLY
2   ARGGLUASNLEUTYRPHEGLNGLYSERGLU
3   ASPGLYSERTYRGLYTHRASPVALTHRARG
4   CYSILECYSGLYPHETHRHISASPASPGLY
5   TYRMETILECYSCYSASPLYSCYSSERVAL
6   TRPGLNHISILEASPCYSMETGLYILEASP
7   ARGGLNHISILEPROASPTHRTYRLEUCYS
8   GLUARGCYSGLNPROARGASNLEUASPLYS
9   GLUARGALAVALLEULEUGLNARGARGLYS
10   ARGGLUASNMETSERASPGLYASP

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: MLL5, [U-13C; U-15N], 0.5 mM; TRIS 10 mM; sodium chloride 300 mM; ZnSO4 10 uM; DTT 1 mM; NaN3 0.01%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 300 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-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

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - peak picking

FMC, Lemak,Steren,Llinas, Arrowsmith - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

PSVS, Bhattacharya and Montelione - validation

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ BAE28389 BAE35839 BAE43262 BAE88379
EMBL CAH93210
GB AAD04721 AAF75564 AAH01296 AAH36286 AAH62583
REF NP_001075920 NP_001094321 NP_061152 NP_081260 NP_891847
SP Q3UG20 Q8IZD2
TPG DAA30676

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts