BMRBj - BMREntryMaster

Found 1 Document (0.665 seconds)

BMRB: 30809

5V9P

Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide

Authors

Longbotham, E.J., Kelly, M.J.S., Fujimori, D.G.

Assembly

Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1

Entity

1. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity 1 (polymer, Thiol state: all other bound), 59 monomers, 6599.504 Da Detail

GSVNFVDLYV CMFCGRGNNE DKLLLCDGCD DSYHTFCLIP PLPDVPKGDW RCPKCVAEE

2. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity 2 (polymer, Thiol state: not present), 10 monomers, 1146.300 Da Detail

ARTKQTARKS

3. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

7876.6216 Da

Max. entity weight

6599.504 Da

Entity Connection

disulfide 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	3:ZN1:ZN
2	disulfide	sing	1:CYS14:SG	3:ZN1:ZN
3	disulfide	sing	1:CYS26:SG	3:ZN1:ZN
4	disulfide	sing	1:CYS29:SG	3:ZN1:ZN
5	disulfide	sing	1:HIS34:ND1	3:ZN1:ZN
6	disulfide	sing	1:CYS37:SG	3:ZN1:ZN
7	disulfide	sing	1:CYS52:SG	3:ZN1:ZN
8	disulfide	sing	1:CYS55:SG	3:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 82.0 %, Completeness (bb): 74.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.0 % (645 of 787)	94.9 % (388 of 409)	66.9 % (204 of 305)	72.6 % (53 of 73)
Backbone	74.0 % (299 of 404)	95.7 % (132 of 138)	56.9 % (115 of 202)	81.3 % (52 of 64)
Sidechain	89.5 % (400 of 447)	94.5 % (256 of 271)	85.6 % (143 of 167)	11.1 % (1 of 9)
Aromatic	96.8 % (60 of 62)	96.8 % (30 of 31)	96.7 % (29 of 30)	100.0 % (1 of 1)
Methyl	93.3 % (56 of 60)	100.0 % (30 of 30)	86.7 % (26 of 30)

1. entity 1

GSVNFVDLYV CMFCGRGNNE DKLLLCDGCD DSYHTFCLIP PLPDVPKGDW RCPKCVAEE

2. entity 2

ARTKQTARKS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	550 uM
8	Histone H3.1	natural abundance	800 uM
9	HEPES	natural abundance	50 mM
10	sodium chloride	natural abundance	150 mM
11	beta-mercaptoethanol	natural abundance	5 mM
12	ZnCl2	natural abundance	0.1 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
13	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	1250 uM
14	Histone H3.1	natural abundance	400 uM
15	HEPES	natural abundance	50 mM
16	sodium chloride	natural abundance	150 mM
17	beta-mercaptoethanol	natural abundance	5 mM
18	ZnCl2	natural abundance	0.1 mM

Release date

2020-11-29

Citation

Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A
Longbotham, J.E., Kelly, M.J.S., Fujimori, D.G.
ACS Chem. Biol. (2021), PubMed 33621062 , DOI 10.1021/acschembio.0c00976 , Abstract

Related entities 1. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity 1, : 1 : 2 : 5 : 206 entities Detail

Experiments performed 11 experiments Detail

1 CBCACONH

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	550 uM
8	Histone H3.1	natural abundance	800 uM
9	HEPES	natural abundance	50 mM
10	sodium chloride	natural abundance	150 mM
11	beta-mercaptoethanol	natural abundance	5 mM
12	ZnCl2	natural abundance	0.1 mM

2 CBCANH

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	550 uM
8	Histone H3.1	natural abundance	800 uM
9	HEPES	natural abundance	50 mM
10	sodium chloride	natural abundance	150 mM
11	beta-mercaptoethanol	natural abundance	5 mM
12	ZnCl2	natural abundance	0.1 mM

3 3D (H)CCCONH-TOCSY

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

4 3D H(CC)(CO)NH-TOCSY

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

5 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

6 2D intra-peptide TOCSY

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
13	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	1250 uM
14	Histone H3.1	natural abundance	400 uM
15	HEPES	natural abundance	50 mM
16	sodium chloride	natural abundance	150 mM
17	beta-mercaptoethanol	natural abundance	5 mM
18	ZnCl2	natural abundance	0.1 mM

7 3D filtered intermolecular NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

8 C HSQC

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

9 N HSQC

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

10 3D NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	900 uM
2	Histone H3.1	natural abundance	4000 uM
3	HEPES	natural abundance	50 mM
4	sodium chloride	natural abundance	150 mM
5	beta-mercaptoethanol	natural abundance	5 mM
6	ZnCl2	natural abundance	0.1 mM

11 2D intra-peptide NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
13	Histone lysine demethylase 5A, KDM5A	[U-13C; U-15N]	1250 uM
14	Histone H3.1	natural abundance	400 uM
15	HEPES	natural abundance	50 mM
16	sodium chloride	natural abundance	150 mM
17	beta-mercaptoethanol	natural abundance	5 mM
18	ZnCl2	natural abundance	0.1 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30809_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	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

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)
1:11:CYS:SG	3:1:ZN:ZN	reduced, CA 58.684, CB 31.995 ppm	unknown	n/a
1:14:CYS:SG	3:1:ZN:ZN	reduced, CA 59.276, CB 31.514 ppm	unknown	n/a
1:26:CYS:SG	4:1:ZN:ZN	reduced, CA 60.964, CB 30.802 ppm	unknown	n/a
1:29:CYS:SG	4:1:ZN:ZN	oxidized 35.8%, reduced 64.2%, CA 59.156, CB 33.363 ppm	unknown	n/a
1:34:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
1:37:CYS:SG	3:1:ZN:ZN	reduced, CA 61.703, CB 31.538 ppm	unknown	n/a
1:52:CYS:SG	4:1:ZN:ZN	reduced, CA 57.116, CB 29.747 ppm	unknown	n/a
1:55:CYS:SG	4:1:ZN:ZN	reduced, CA 64.513, CB 29.336 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr30809_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	704		98.3 (chain: 1, length: 59), 100.0 (chain: 2, length: 10)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 59, Sequence coverage: 98.3%
  - Entity_assembly_ID: 2, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 450
  - ¹³C chemical shifts: 201
  - ¹⁵N chemical shifts: 53
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- 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
  - Chain_ID: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	345	332	96.2
¹³C chemical shifts	262	201	76.7
¹⁵N chemical shifts	60	53	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	118	114	96.6
¹³C chemical shifts	118	58	49.2
¹⁵N chemical shifts	54	52	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	227	218	96.0
¹³C chemical shifts	144	143	99.3
¹⁵N chemical shifts	6	1	16.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	27	100.0
¹³C chemical shifts	27	27	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	30	96.8
¹³C chemical shifts	30	29	96.7
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	56	87.5
¹³C chemical shifts	43	0	0.0
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	18	90.0
¹³C chemical shifts	20	0	0.0
¹⁵N chemical shifts	10	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	38	86.4
¹³C chemical shifts	23	0	0.0
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	0	0.0

Keywords Epigenetics, GENE REGULATION, H3, KDM5A, PHD

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Found 1 Document (0.665 seconds)

BMRB: 30809

Sample #1

Sample #2

Sample #3

Related entities 1. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity 1, : 1 : 2 : 5 : 206 entities Detail

Experiments performed 11 experiments Detail

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Chemical shift validation 5 contents Detail