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Biological Magnetic Resonance Data Bank


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BMRB Entry 25130

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25130
MolProbity Validation Chart

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Title: Solution structure of LEDGF/p75 IBD in complex with MLL1 peptide (140-160)   PubMed: 25082813

Deposition date: 2014-08-05 Original release date: 2014-08-25

Authors: Cermakova, Katerina; Tesina, Petr; Demeulemeester, Jonas; El Ashkar, Sara; Mereau, Helene; Schwaller, Juerg; Rezacova, Pavlina; Veverka, Vaclav; De Rijck, Jan

Citation: Cermakova, Katerina; Tesina, Petr; Demeulemeester, Jonas; El Ashkar, Sara; Mereau, Helene; Schwaller, Juerg; Rezacova, Pavlina; Veverka, Vaclav; De Rijck, Jan. "Validation and Structural Characterization of the LEDGF/p75-MLL Interface as a New Target for the Treatment of MLL-Dependent Leukemia."  Cancer Res. 74, 5139-5151 (2014).

Assembly members:
MLL1_140-160, polymer, 21 residues, 2272.364 Da.
IBD, polymer, 88 residues, 10260.019 Da.

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
MLL1_140-160: GGSGEDEQFLGFGSDEEVRV R
IBD: SNAASRETSMDSRLQRIHAE IKNSLKIDNLDVNRCIEALD ELASLQVTMQQAQKHTEMIT TLKKIRRFKVSQVIMEKSTM LYNKFKNM

Data sets:
Data typeCount
1H chemical shifts734
13C chemical shifts372
15N chemical shifts89

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1MLL1 peptide (140-160)1
2LEDGF/p75 IBD2

Entities:

Entity 1, MLL1 peptide (140-160) 21 residues - 2272.364 Da.

1   GLYGLYSERGLYGLUASPGLUGLNPHELEU
2   GLYPHEGLYSERASPGLUGLUVALARGVAL
3   ARG

Entity 2, LEDGF/p75 IBD 88 residues - 10260.019 Da.

1   SERASNALAALASERARGGLUTHRSERMET
2   ASPSERARGLEUGLNARGILEHISALAGLU
3   ILELYSASNSERLEULYSILEASPASNLEU
4   ASPVALASNARGCYSILEGLUALALEUASP
5   GLULEUALASERLEUGLNVALTHRMETGLN
6   GLNALAGLNLYSHISTHRGLUMETILETHR
7   THRLEULYSLYSILEARGARGPHELYSVAL
8   SERGLNVALILEMETGLULYSSERTHRMET
9   LEUTYRASNLYSPHELYSASNMET

Samples:

sample_1: MLL1_140-160 0.5 mM; IBD, [U-13C; U-15N], 0.5 mM; HEPES 25 mM; sodium chloride 100 mM; beta-mercaptoethanol 0.05%

sample_conditions_1: temperature: 298 K; pH: 7; pressure: 1 atm; ionic strength: 125 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

YASARA, YASARA - refinement

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAA03407 BAJ78791 BAK63380
EMBL CAA93625 CAC34944
GB AAA58669 AAA62593 AAC37520 AAC95283 AAC95284 AAB52589 AAC25167 AAC97946 AAF25870 AAH02260
PIR A48205
PRF 1919460A
REF NP_001074518 NP_001184033 NP_005924 XP_001093874 XP_003253537 NP_001009372 NP_001075982 NP_001121689 NP_001137364 NP_001193405
SP P55200 Q03164 O75475 Q66T72 Q812D1 Q8MJG1 Q99JF8
TPG DAA22311 DAA26946
BMRB 25171
AlphaFold Q03164 P55200 Q8MJG1 O75475 Q66T72 Q812D1 Q99JF8

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