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BMRB: 16210

2KGI

Solution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3

Authors

Song, J., Wang, Z., Patel, D.J.

Assembly

JARID1A PHD finger 3

Entity

1. JARID1A PHD finger 3 (polymer, Thiol state: free and other bound), 52 monomers, 5798.455 Da Detail

SVCAAQNCQR PCKDKVDWVQ CDGGCDEWFH QVCVGVSPEM AENEDYICIN CA

2. ZN (non-polymer), 65.409 × 2 Da
3. H3(1-9)K4me3 (polymer, Thiol state: not present), 9 monomers, 1102.310 Da Detail

ARTXQTARK

Total weight

7031.583 Da

Max. entity weight

5798.455 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 85.3 %, Completeness (bb): 88.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.3 % (561 of 658)	87.1 % (298 of 342)	82.3 % (204 of 248)	86.8 % (59 of 68)
Backbone	88.2 % (314 of 356)	95.0 % (115 of 121)	84.2 % (149 of 177)	86.2 % (50 of 58)
Sidechain	82.5 % (296 of 359)	82.8 % (183 of 221)	81.3 % (104 of 128)	90.0 % (9 of 10)
Aromatic	78.3 % (36 of 46)	78.3 % (18 of 23)	76.2 % (16 of 21)	100.0 % (2 of 2)
Methyl	91.7 % (44 of 48)	95.8 % (23 of 24)	87.5 % (21 of 24)

1. JARID1A PHD finger 3

SVCAAQNCQR PCKDKVDWVQ CDGGCDEWFH QVCVGVSPEM AENEDYICIN CA

3. H3(1-9)K4me3

ARTXQTARK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details This sample was used to measure N-H RDCs of JARID1A PHD finger 3

#	Name	Isotope labeling	Concentration
6	JARID1A PHD finger 3	[U-100% 15N]	0.2 ~ 0.5 mM
7	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
8	DTT	natural abundance	5 mM
9	ZINC ION	natural abundance	1 mM
10	MOPS	natural abundance	10 mM
11	bacteriophage Pf1	natural abundance	12 mg/mL

Protein Blocks Logo

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

Release date

2009-05-28

Citation

Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger
Wang, G.G., Song, J., Wang, Z., Dormann, H.L., Casadio, F., Li, H., Luo, J., Patel, D.J., Allis, C.D.
Nature (2009), 459, 847-851, PubMed 19430464 , DOI 10.1038/nature08036 , Abstract

Related entities 1. JARID1A PHD finger 3, : 3 : 95 entities Detail

Experiments performed 13 experiments Detail

1 1H,15N-HSQC

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

2 1H,13C-HSQC

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

3 HNCACB

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

4 HBHACONH

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

5 CBCACONH

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

6 2D 1H, 1H-NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

7 HCCHTOCSY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

8 15N-EDITED 1H,1H-NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

9 13C-EDITED 1H,1H-NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

10 15N IPAP HSQC

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

11 13C,15N-FILTERED, 13C-EDITED 1H,1H-NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

12 13C,15N-FILTERED, 2D 1H,1H-NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O

#	Name	Isotope labeling	Concentration
1	JARID1A PHD finger 3	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
3	DTT	natural abundance	0.5 mM
4	ZINC ION	natural abundance	1 mM
5	sodium phosphate	natural abundance	20 mM

13 15N IPAP HSQC

Instrument

Bruker DMX - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.0, Details This sample was used to measure N-H RDCs of JARID1A PHD finger 3

#	Name	Isotope labeling	Concentration
6	JARID1A PHD finger 3	[U-100% 15N]	0.2 ~ 0.5 mM
7	H3(1-9)K4Me3	natural abundance	0.2 ~ 0.5 mM
8	DTT	natural abundance	5 mM
9	ZINC ION	natural abundance	1 mM
10	MOPS	natural abundance	10 mM
11	bacteriophage Pf1	natural abundance	12 mg/mL

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16210_2kgi.nef
Input source #2: Coordindates	2kgi.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)
2:3:THR:C	2:4:M3L:N	unknown	unknown	n/a
2:4:M3L:C	2:5:GLN:N	unknown	unknown	n/a
1:3:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:8:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:21:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:25:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:30:HIS:ND1	3:2:ZN:ZN	unknown	unknown	n/a
1:33:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:48:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:51:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	304	M3L	N-TRIMETHYLLYSINE	Assigned chemical shifts, Coordinates
C	1	ZN	ZINC ION	None
C	2	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--
SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA
||||||||||||||||||||||||||||||||||||||||||||||||||||
SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA

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

---------
ARTXQTARK
|||||||||
ARTXQTARK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	52	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_16210_2kgi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	10		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	576		100.0 (chain: A, length: 52), 100.0 (chain: B, length: 9)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	846 (1)	noe	98.1 (chain: A, length: 52), 66.7 (chain: B, length: 9)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	18 (1)	hbond	26.9 (chain: A, length: 52), 22.2 (chain: B, length: 9)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	59 (59)	.	86.5 (chain: A, length: 52)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	47 (47)	.	90.4 (chain: A, length: 52)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 203
  - ¹H chemical shifts: 315
  - ¹⁵N chemical shifts: 58
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	214	203	94.9
¹H chemical shifts	292	273	93.5
¹⁵N chemical shifts	60	58	96.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	104	99	95.2
¹H chemical shifts	105	103	98.1
¹⁵N chemical shifts	50	49	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	110	104	94.5
¹H chemical shifts	187	170	90.9
¹⁵N chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	21	20	95.2
¹H chemical shifts	21	20	95.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	21	16	76.2
¹H chemical shifts	23	18	78.3
¹⁵N chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	34	0	0.0
¹H chemical shifts	63	42	66.7
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	16	0	0.0
¹H chemical shifts	18	16	88.9
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	18	0	0.0
¹H chemical shifts	45	26	57.8
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	7	0	0.0
¹H chemical shifts	7	4	57.1

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 98.1%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 66.7%
- Total number of restraints: 846
- Weight of restraints: 1.0 (846)
- Potential type of restraints: square-well-parabolic (846)
- Range of distance target values: 1.24, 3.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 26.9%
    - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 22.2%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: square-well-parabolic (18)
  - Range of distance target values: 1.15, 1.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 86.5%
- Total number of restraints: 59
- Total number of restraints per polymer type: 59
- Weight of restraints: 1.0 (59)
- Potential type of restraints: square-well-parabolic (59)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 90.4%
- Total number of restraints: 47
- Potential type of restraints: undefined (47)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords histone modification, JARID1A, leukemia, PHD finger

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Found 1 Document (0.68 seconds)

BMRB: 16210

Sample #1

Sample #2

Related entities 1. JARID1A PHD finger 3, : 3 : 95 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 6 contents Detail