BMRBj - BMREntryMaster

Found 1 Document (0.666 seconds)

BMRB: 11606

2RVM

Solution structure of the chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide

Authors

Kawaguchi, A., Nishimura, Y.

Assembly

Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide

Entity

1. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 1 (polymer, Thiol state: all free), 83 monomers, 10149.89 Da Detail

GSHMGKKTKR TADXXXXEDE EEYVVEKVLD RRMVKGQVEY LLKWKGFSEE HNTWEPEKNL DCPELISEFM KKYKKMKEGE NNK

2. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 2 (polymer, Thiol state: not present), 18 monomers, 2020.319 Da Detail

ARTKQTARXS TGGKAPRY

Total weight

12170.209 Da

Max. entity weight

10149.89 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 78.2 %, Completeness: 77.9 %, Completeness (bb): 81.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.9 % (920 of 1181)	75.7 % (476 of 629)	80.2 % (357 of 445)	81.3 % (87 of 107)
Backbone	81.6 % (465 of 570)	80.1 % (157 of 196)	82.2 % (231 of 281)	82.8 % (77 of 93)
Sidechain	75.6 % (529 of 700)	73.7 % (319 of 433)	79.1 % (200 of 253)	71.4 % (10 of 14)
Aromatic	81.0 % (68 of 84)	81.0 % (34 of 42)	80.0 % (32 of 40)	100.0 % (2 of 2)
Methyl	82.8 % (53 of 64)	81.3 % (26 of 32)	84.4 % (27 of 32)

1. entity 1

GSHMGKKTKR TADXXXXEDE EEYVVEKVLD RRMVKGQVEY LLKWKGFSEE HNTWEPEKNL DCPELISEFM KKYKKMKEGE NNK

2. entity 2

ARTKQTARXS TGGKAPRY

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
9	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
10	potassium phosphate	"natural abundance	buffer	20 mM
11	sodium chloride	natural abundance	salt	10 mM
12	DTT	natural abundance		5 mM
13	D2O	[U-2H]	solvent	100 %

Chem. Shift Complete2

Sequence coverage: 23.8 %, Completeness: 44.3 %, Completeness (bb): 46.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	44.3 % (1046 of 2362)	45.9 % (578 of 1258)	42.0 % (374 of 890)	43.9 % (94 of 214)
Backbone	46.0 % (524 of 1140)	49.0 % (192 of 392)	44.1 % (248 of 562)	45.2 % (84 of 186)
Sidechain	43.0 % (602 of 1400)	44.6 % (386 of 866)	40.7 % (206 of 506)	35.7 % (10 of 28)
Aromatic	42.9 % (72 of 168)	45.2 % (38 of 84)	40.0 % (32 of 80)	50.0 % (2 of 4)
Methyl	47.7 % (61 of 128)	53.1 % (34 of 64)	42.2 % (27 of 64)

1. entity 1

GSHMGKKTKR TADXXXXEDE EEYVVEKVLD RRMVKGQVEY LLKWKGFSEE HNTWEPEKNL DCPELISEFM KKYKKMKEGE NNK

2. entity 2

ARTKQTARXS TGGKAPRY

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

Release date

2015-12-20

Citation

Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail
Shimojo, H., Kawaguchi, A., Oda, T., Hashiguchi, N., Omori, S., Moritsugu, K., Kidera, A., Hiragami-Hamada, K., Nakayama, J., Sato, M., Nishimura, Y.
Sci. Rep. (2016), 6, 22527-22527, PubMed 26934956 , DOI 10.1038/srep22527 , Abstract

Related entities 1. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 1, : 1 : 1 : 3 : 21 entities Detail

Related entities 2. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 2, : 107 : 37 entities Detail

Interaction partners 2. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 2, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
9	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
10	potassium phosphate	"natural abundance	buffer	20 mM
11	sodium chloride	natural abundance	salt	10 mM
12	DTT	natural abundance		5 mM
13	D2O	[U-2H]	solvent	100 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
9	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
10	potassium phosphate	"natural abundance	buffer	20 mM
11	sodium chloride	natural abundance	salt	10 mM
12	DTT	natural abundance		5 mM
13	D2O	[U-2H]	solvent	100 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

8 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

9 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

10 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

11 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
9	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
10	potassium phosphate	"natural abundance	buffer	20 mM
11	sodium chloride	natural abundance	salt	10 mM
12	DTT	natural abundance		5 mM
13	D2O	[U-2H]	solvent	100 %

13 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
2	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	10 mM
5	DTT	natural abundance		5 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

14 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
9	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
10	potassium phosphate	"natural abundance	buffer	20 mM
11	sodium chloride	natural abundance	salt	10 mM
12	DTT	natural abundance		5 mM
13	D2O	[U-2H]	solvent	100 %

15 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
8	HP1alpha	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
9	H3K9me3	[U-99% 13C; U-99% 15N]	protein	0.0 ~ 0.0 mM
10	potassium phosphate	"natural abundance	buffer	20 mM
11	sodium chloride	natural abundance	salt	10 mM
12	DTT	natural abundance		5 mM
13	D2O	[U-2H]	solvent	100 %

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr11606_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
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)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	14	SEP	PHOSPHOSERINE	Assigned chemical shifts
1	15	SEP	PHOSPHOSERINE	Assigned chemical shifts
1	16	SEP	PHOSPHOSERINE	Assigned chemical shifts
1	17	SEP	PHOSPHOSERINE	Assigned chemical shifts
2	9	M3L	N-TRIMETHYLLYSINE	Assigned chemical shifts

Content subtype: bmr11606_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1008	97.6 (chain: 1, length: 83)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	103	88.9 (chain: 2, length: 18)
1	Chemical shift references	chemical_shift_reference_1	OK	3	No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 83, Sequence coverage: 97.6%
- Total number of assignments
  - ¹H chemical shifts: 548
  - ¹³C chemical shifts: 372
  - ¹⁵N chemical shifts: 88
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: 1
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 18, Sequence coverage: 88.9%
- Total number of assignments
  - ¹H chemical shifts: 103
- Completeness of assignments
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 2

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	ARG	CZ	159.526
17	SEP	C	173.887
31	ARG	CZ	158.967
32	ARG	CZ	158.138
37	GLN	CD	180.711
44	TRP	CE2	139.029
52	ASN	CG	174.308
54	TRP	CE2	139.051
59	ASN	CG	176.707
81	ASN	CG	177.196
82	ASN	CG	177.288

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	544	488	89.7
¹³C chemical shifts	382	361	94.5
¹⁵N chemical shifts	91	88	96.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	169	161	95.3
¹³C chemical shifts	162	158	97.5
¹⁵N chemical shifts	81	78	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	375	327	87.2
¹³C chemical shifts	220	203	92.3
¹⁵N chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	30	100.0
¹³C chemical shifts	30	30	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	34	89.5
¹³C chemical shifts	36	32	88.9
¹⁵N chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	86	75.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	37	26	70.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	60	77.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Keywords chromodomain, hp1alpha

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Found 1 Document (0.666 seconds)

BMRB: 11606

Sample #1

Sample #2

Sample

Related entities 1. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 1, : 1 : 1 : 3 : 21 entities Detail

Related entities 2. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 2, : 107 : 37 entities Detail

Interaction partners 2. Chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide, entity 2, : 1 interactors Detail

Experiments performed 15 experiments Detail

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Chemical shift validation 5 contents Detail