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BMRB: 17071

2L11

Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide

Authors

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

Assembly

Cbx3 H3K9me3 complex

Entity

1. Cbx3 (polymer, Thiol state: all free), 54 monomers, 6347.033 Da Detail

GEFVVEKVLD RRVVNGKVEY FLKWKGFTDA DNTWEPEENL DCPELIEAFL NSQK

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

ARTKQTARXS TGGKA

Total weight

7950.877 Da

Max. entity weight

6347.033 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 87.0 %, Completeness: 80.0 %, Completeness (bb): 77.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.0 % (646 of 807)	82.7 % (349 of 422)	77.5 % (241 of 311)	75.7 % (56 of 74)
Backbone	77.0 % (311 of 404)	77.7 % (108 of 139)	77.4 % (154 of 199)	74.2 % (49 of 66)
Sidechain	82.8 % (386 of 466)	85.2 % (241 of 283)	78.9 % (138 of 175)	87.5 % (7 of 8)
Aromatic	83.3 % (60 of 72)	97.2 % (35 of 36)	67.6 % (23 of 34)	100.0 % (2 of 2)
Methyl	86.8 % (59 of 68)	91.2 % (31 of 34)	82.4 % (28 of 34)

1. Cbx3

GEFVVEKVLD RRVVNGKVEY FLKWKGFTDA DNTWEPEENL DCPELIEAFL NSQK

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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2L11, 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. Cbx3, : 3 : 106 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 14 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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

4 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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

5 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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

8 3D-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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

9 3D-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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

10 3D -13C-aromatic-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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

11 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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

12 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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

13 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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

14 3D-aromatic 1H-13C-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	Cbx3	[U-13C; U-15N]		0.43 mM
2	H3K9me3	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium chloride	natural abundance		200 mM
5	DTT	natural abundance		2 mM
6	TCEP	natural abundance		1 mM
7	PMSF	natural abundance		0.5 mM
8	Benzamidine	natural abundance		1 mM
9	H2O	natural abundance		90 %
10	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_17071_2l11.nef
Input source #2: Coordindates	2l11.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	Coordinates

Sequence alignments

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

--------10--------20--------30--------40--------50----
GEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK
||||||||||||||||||||||||||||||||||||||||||||||||||||||
GEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK

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	54	0	0	100.0
B	B	15	0	0	100.0

Content subtype: combined_17071_2l11.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	659		100.0 (chain: A, length: 54), 40.0 (chain: B, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	1500 (1)	noe	98.1 (chain: A, length: 54), 26.7 (chain: B, length: 15)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	12 (1)	hbond	11.1 (chain: A, length: 54), 13.3 (chain: B, length: 15)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	68 (68)	.	92.6 (chain: A, length: 54)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 40.0%
- Total number of assignments
  - ¹H chemical shifts: 362
  - ¹³C chemical shifts: 241
  - ¹⁵N chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: 54, Sequence coverage: 98.1%
  - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 26.7%
- Total number of restraints: 1500
- Weight of restraints: 1.0 (1500)
- Potential type of restraints: square-well-parabolic (1500)
- 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_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 11.1%
    - Entity_assembly_ID: B, Chain length: 15, Sequence coverage: 13.3%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: square-well-parabolic (12)
  - 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 92.6%
- 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