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BMRB: 17072

2L12

Solution NMR structure of the chromobox protein 7 with H3K9me3

Authors

Kaustov, L., Lemak, A., Gutmanas, A., Fares, C., Quang, H., Loppnau, P., Min, J., Edwards, A., Arrowsmith, C.

Assembly

Cbx7 H3K9me3 complex

Entity

1. Cbx7 (polymer, Thiol state: not present), 56 monomers, 6803.746 Da Detail

GEQVFAVESI RKKRVRKGKV EYLVKWKGWP PKYSTWEPEE HILDPRLVMA YEEKEE

2. H3K9me3 (polymer, Thiol state: not present), 15 monomers, 1603.844 Da Detail

ARTKQTARXS TGGKA

Total weight

8407.59 Da

Max. entity weight

6803.746 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 84.5 %, Completeness: 78.9 %, Completeness (bb): 72.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.9 % (683 of 866)	83.3 % (384 of 461)	76.0 % (254 of 334)	63.4 % (45 of 71)
Backbone	72.3 % (298 of 412)	75.2 % (106 of 141)	72.7 % (149 of 205)	65.2 % (43 of 66)
Sidechain	84.2 % (437 of 519)	86.9 % (278 of 320)	80.9 % (157 of 194)	40.0 % (2 of 5)
Aromatic	86.5 % (64 of 74)	97.3 % (36 of 37)	76.5 % (26 of 34)	66.7 % (2 of 3)
Methyl	85.5 % (53 of 62)	90.3 % (28 of 31)	80.6 % (25 of 31)

1. Cbx7

GEQVFAVESI RKKRVRKGKV EYLVKWKGWP PKYSTWEPEE HILDPRLVMA YEEKEE

2. H3K9me3

ARTKQTARXS TGGKA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2L12, Strand ID: A, B Detail

Release date

2010-08-17

Citation

Recognition and specificity determinants of the human cbx chromodomains
Kaustov, L., Ouyang, H., Amaya, M., Lemak, A., Nady, N., Duan, S., Wasney, G.A., Li, Z., Vedadi, M., Schapira, M., Min, J., Arrowsmith, C.H.
J. Biol. Chem. (2011), 286, 521-529, PubMed 21047797 , DOI 10.1074/jbc.M110.191411 , Abstract

Related entities 1. Cbx7, : 3 : 69 entities Detail

Related entities 2. H3K9me3, : 109 : 17 entities Detail

Interaction partners 2. H3K9me3, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

8 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

11 13C/15N-filtered/edited NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

12 3D aro 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	Cbx7	[U-13C; U-15N]		0.5 mM
2	H3K9me3	natural abundance		2.5 mM
3	sodium phosphate	natural abundance		10 mM
4	sodium chloride	natural abundance		300 mM
5	TCEP	natural abundance		1 mM
6	Benzamidine	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17072_2l12.nef
Input source #2: Coordindates	2l12.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:8:ARG:C	2:9:M3L:N	unknown	unknown	n/a
2:9:M3L:C	2:10:SER:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	9	M3L	N-TRIMETHYLLYSINE	Assigned chemical shifts, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50------
GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10-----
ARTKQTARXSTGGKA
|||||||||||||||
ARTKQTARXSTGGKA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0
B	B	15	0	0	100.0

Content subtype: combined_17072_2l12.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	680		96.4 (chain: A, length: 56), 46.7 (chain: B, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	1584 (1)	noe	96.4 (chain: A, length: 56), 26.7 (chain: B, length: 15)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	hbond	13.3 (chain: B, length: 15)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	68 (68)	.	87.5 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 96.4%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 46.7%
- Total number of assignments
  - ¹H chemical shifts: 385
  - ¹³C chemical shifts: 251
  - ¹⁵N chemical shifts: 44
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 96.4%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 26.7%
- Total number of restraints: 1584
- Weight of restraints: 1.0 (1584)
- Potential type of restraints: square-well-parabolic (1584)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 13.3%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 87.5%
- Total number of restraints: 68
- Total number of restraints per polymer type: 68
- Weight of restraints: 1.0 (68)
- Potential type of restraints: square-well-parabolic (68)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords chromodomain