BMRB Entry 18000

Name: Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology
Published: 2012-01-17

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PDB ID: 2lkm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18000
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology PubMed: 22244764

Deposition date: 2011-10-16 Original release date: 2012-01-17

Authors: Xie, Tao; Radhakrishnan, Ishwar

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).

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

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

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

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	870
15N chemical shifts	204
1H chemical shifts	1387

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Pf1	1
2	MRG15	2

Entities:

Entity 1, Pf1 42 residues - 4721.391 Da.

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

1

ASP

TYR

VAL

GLN

PRO

GLN

LEU

ARG

PRO

2

PHE

GLU

LEU

ILE

ALA

MET

GLU

3

ARG

ASN

PRO

THR

GLN

PHE

GLN

LEU

PRO

ASN

4

GLU

LEU

THR

CYS

THR

ALA

LEU

PRO

GLY

5

SER

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

SER

ASN

ALA

GLU

VAL

LYS

VAL

LYS

ILE

PRO

2

GLU

LEU

LYS

PRO

TRP

LEU

VAL

ASP

3

TRP

ASP

LEU

ILE

THR

ARG

GLN

LYS

GLN

LEU

4

PHE

TYR

LEU

PRO

ALA

LYS

ASN

VAL

ASP

5

SER

ILE

LEU

GLU

ASP

TYR

ALA

ASN

TYR

ARG

6

LYS

SER

ARG

GLY

ASN

THR

ASP

ASN

LYS

GLU

7

TYR

ALA

VAL

ASN

GLU

VAL

ALA

GLY

ILE

8

LYS

GLU

TYR

PHE

ASN

VAL

MET

LEU

GLY

THR

9

GLN

LEU

TYR

LYS

PHE

GLU

ARG

PRO

GLN

10

TYR

ALA

GLU

ILE

LEU

ALA

ASP

HIS

PRO

ASP

11

ALA

PRO

MET

SER

GLN

VAL

TYR

GLY

ALA

PRO

12

HIS

LEU

ARG

LEU

PHE

VAL

ARG

ILE

GLY

13

ALA

MET

LEU

ALA

TYR

THR

PRO

LEU

ASP

GLU

14

LYS

SER

LEU

ALA

LEU

ASN

TYR

LEU

15

HIS

ASP

PHE

LEU

LYS

TYR

LEU

ALA

LYS

ASN

16

SER

ALA

THR

LEU

PHE

SER

ALA

SER

ASP

TYR

17

GLU

VAL

ALA

PRO

GLU

TYR

HIS

ARG

LYS

18

ALA

VAL

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNCA	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
3D HCACO	sample_4	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1

Software:

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

ARIA v1.2, Linge, O, . - structure solution

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

NMR spectrometers:

Varian INOVA 600 MHz

BMRB	17485
PDB	2L9S 2LKM 2AQL 2F5J 2LKM
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

Biological Magnetic Resonance Data Bank