BMRB Entry 18000

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18000
MolProbity Validation Chart

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Title:
Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology
Deposition date:
2011-10-16
Original release date:
2012-01-17
Authors:
Xie, Tao; Radhakrishnan, Ishwar
Citation:

Citation: Xie, Tao; Graveline, Richard; Kumar, Ganesan Senthil; Zhang, Yongbo; Krishnan, Arvind; David, Gregory; Radhakrishnan, Ishwar. "Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology."  Structure 20, 151-160 (2012).
PubMed: 22244764

Assembly members:

Assembly members:
Pf1, polymer, 42 residues, 4721.391 Da.
MRG15, polymer, 172 residues, 19870.898 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: pMCSG7

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Pf1: DYVQPQLRRPFELLIAAAME RNPTQFQLPNELTCTTALPG SS
MRG15: SNAEVKVKIPEELKPWLVDD WDLITRQKQLFYLPAKKNVD SILEDYANYRKSRGNTDNKE YAVNEVVAGIKEYFNVMLGT QLLYKFERPQYAEILADHPD APMSQVYGAPHLLRLFVRIG AMLAYTPLDEKSLALLLNYL HDFLKYLAKNSATLFSASDY EVAPPEYHRKAV

Data sets:
Data typeCount
13C chemical shifts870
15N chemical shifts204
1H chemical shifts1387

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Pf11
2MRG152

Entities:

Entity 1, Pf1 42 residues - 4721.391 Da.

This is the MRG binding domain of PHD factor 1 (Pf1) protein

1   ASPTYRVALGLNPROGLNLEUARGARGPRO
2   PHEGLULEULEUILEALAALAALAMETGLU
3   ARGASNPROTHRGLNPHEGLNLEUPROASN
4   GLULEUTHRCYSTHRTHRALALEUPROGLY
5   SERSER

Entity 2, MRG15 172 residues - 19870.898 Da.

Residues 1-3 is from a non-native affinity tag. This is the MRG domain of MRG15

1   SERASNALAGLUVALLYSVALLYSILEPRO
2   GLUGLULEULYSPROTRPLEUVALASPASP
3   TRPASPLEUILETHRARGGLNLYSGLNLEU
4   PHETYRLEUPROALALYSLYSASNVALASP
5   SERILELEUGLUASPTYRALAASNTYRARG
6   LYSSERARGGLYASNTHRASPASNLYSGLU
7   TYRALAVALASNGLUVALVALALAGLYILE
8   LYSGLUTYRPHEASNVALMETLEUGLYTHR
9   GLNLEULEUTYRLYSPHEGLUARGPROGLN
10   TYRALAGLUILELEUALAASPHISPROASP
11   ALAPROMETSERGLNVALTYRGLYALAPRO
12   HISLEULEUARGLEUPHEVALARGILEGLY
13   ALAMETLEUALATYRTHRPROLEUASPGLU
14   LYSSERLEUALALEULEULEUASNTYRLEU
15   HISASPPHELEULYSTYRLEUALALYSASN
16   SERALATHRLEUPHESERALASERASPTYR
17   GLUVALALAPROPROGLUTYRHISARGLYS
18   ALAVAL

Samples:

sample_1: Pf1, [U-100% 13C; U-100% 15N], 0.9 mM; MRG15 0.9 mM; sodium phosphate 50 mM; D2O, [U-100% 2H], 10%; DTT, [U-2H], 5 mM; sodium azide 0.2%; H2O 90%; D2O 10%

sample_2: Pf1, [U-100% 13C; U-100% 15N], 0.9 mM; MRG15 0.9 mM; potassium chloride 50 mM; D2O, [U-100% 2H], 100%; DTT, [U-2H], 5 mM; sodium azide 0.2%; D2O 100%

sample_3: Pf1 0.9 mM; MRG15, [U-100% 13C; U-100% 15N], 0.9 mM; sodium phosphate 50 mM; D2O, [U-100% 2H], 10%; DTT, [U-2H], 5 mM; sodium azide 0.2%; H2O 90%; D2O 10%

sample_4: Pf1 0.9 mM; MRG15, [U-100% 13C; U-100% 15N], 0.9 mM; sodium phosphate 50 mM; D2O, [U-100% 2H], 100%; DTT, [U-2H], 5 mM; sodium azide 0.2%; D2O 100%

sample_conditions_1: pH: 6.8; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_4isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D HCACOsample_4isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_4isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1

Software:

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

ARIA v1.2, Linge, O'Donoghue and Nilges - structure solution

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

BMRB 17485
PDB
DBJ BAD18713 BAE00370 BAE24837 BAE33212 BAE41602 BAB30219 BAB58904 BAC37546 BAD90270 BAE00783
GB AAH01657 AAH43080 AAI10883 AAI21044 AAI21045 AAD20058 AAD20970 AAD29872 AAF29033 AAF80854
REF NP_001013135 NP_001028733 NP_001179060 NP_001253214 NP_001277060 NP_001011999 NP_001030525 NP_001034236 NP_001127679 NP_001240678
SP Q5SPL2 Q96QT6 P60762 Q5NVP9 Q6AYU1 Q9UBU8
TPG DAA18992 DAA17605
EMBL CAB70879 CAI29614
AlphaFold Q5SPL2 Q96QT6 P60762 Q5NVP9 Q6AYU1 Q9UBU8

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