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BMRB: 18764

4BD3

Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity

Authors

Lapinaite, A., Simon, B., Carlomagno, T.

Assembly

Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity

Entity

1. PHD FINGER PROTEIN 19 (polymer, Thiol state: all free), 58 monomers, 6712.577 Da Detail

SKLTEGQYVL CRWTDGLYYL GKIKRVSSSK QSCLVTFEDN SKYWVLWKDI QHAGVPGE

2. HISTONE H3 (polymer, Thiol state: not present), 11 monomers, 1256.475 Da Detail

ATGGVXKPHR Y

Total weight

7969.0522 Da

Max. entity weight

6712.577 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

ARIA

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 84.1 %, Completeness: 73.0 %, Completeness (bb): 70.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.0 % (594 of 814)	77.8 % (329 of 423)	64.8 % (206 of 318)	80.8 % (59 of 73)
Backbone	70.8 % (286 of 404)	82.3 % (116 of 141)	58.9 % (116 of 197)	81.8 % (54 of 66)
Sidechain	76.4 % (360 of 471)	75.5 % (213 of 282)	78.0 % (142 of 182)	71.4 % (5 of 7)
Aromatic	55.3 % (52 of 94)	57.4 % (27 of 47)	54.5 % (24 of 44)	33.3 % (1 of 3)
Methyl	86.8 % (59 of 68)	88.2 % (30 of 34)	85.3 % (29 of 34)

1. PHD FINGER PROTEIN 19

SKLTEGQYVL CRWTDGLYYL GKIKRVSSSK QSCLVTFEDN SKYWVLWKDI QHAGVPGE

2. HISTONE H3

ATGGVXKPHR Y

Show sample condition

Sample

Solvent system 90% WATER/10% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 7.000, Details 0.1-0.6 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PHD FINGER PROTEIN 19	[U-13C; U-15N]		0.1 ~ 0.6 mM
2	HISTONE H3	[U-13C; U-15N]		0.1 ~ 0.6 mM

Chem. Shift Complete2

Sequence coverage: 31.9 %, Completeness: 42.3 %, Completeness (bb): 41.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	42.3 % (688 of 1628)	47.0 % (398 of 846)	35.5 % (226 of 636)	43.8 % (64 of 146)
Backbone	41.0 % (331 of 808)	49.3 % (139 of 282)	33.8 % (133 of 394)	44.7 % (59 of 132)
Sidechain	43.8 % (413 of 942)	45.9 % (259 of 564)	40.9 % (149 of 364)	35.7 % (5 of 14)
Aromatic	29.3 % (55 of 188)	31.9 % (30 of 94)	27.3 % (24 of 88)	16.7 % (1 of 6)
Methyl	47.1 % (64 of 136)	50.0 % (34 of 68)	44.1 % (30 of 68)

1. PHD FINGER PROTEIN 19

SKLTEGQYVL CRWTDGLYYL GKIKRVSSSK QSCLVTFEDN SKYWVLWKDI QHAGVPGE

2. HISTONE H3

ATGGVXKPHR Y

Show sample condition

Sample

Solvent system 90% WATER/10% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 7.000, Details 0.1-0.6 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PHD FINGER PROTEIN 19	[U-13C; U-15N]		0.1 ~ 0.6 mM
2	HISTONE H3	[U-13C; U-15N]		0.1 ~ 0.6 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 4BD3, Strand ID: A, B Detail

Release date

2012-10-28

Citation

Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity
Ballare, C., Lange, M., Lapinaite, A., Martin, G., Morey, L., Pascual, G., Liefke, R., Simon, B., Shi, Y., Gozani, O., Carlomagno, T., Benitah, S., Di Croce, L.
Nat. Struct. Mol. Biol. (2012), 19, 1257-1265, PubMed 23104054 , DOI 10.1038/nsmb.2434 , Abstract

Entries sharing articles Swiss-Prot: 5 entries Detail

  Swiss-Prot: Q5T6S3 released on 2008-02-05
    Title PHF19_HUMAN Entity PHD finger protein 19
  Swiss-Prot: Q9CXG9 released on 2008-02-05
    Title PHF19_MOUSE Entity PHD finger protein 19
  Swiss-Prot: Q24459 released on 2004-05-10
    Title PCL_DROME Entity Polycomb protein Pcl
  Swiss-Prot: Q02395 released on 2000-12-01
    Title MTF2_MOUSE Entity Metal-response element-binding transcription factor 2
  Swiss-Prot: Q9Z1B8 released on 2000-12-01
    Title PHF1_MOUSE Entity PHD finger protein 1

Related entities 1. PHD FINGER PROTEIN 19, : 2 : 22 entities Detail

Related entities 2. HISTONE H3, : 39 : 28 entities Detail

Interaction partners 1. PHD FINGER PROTEIN 19, : 15 interactors Detail

More details for 15 interactors identified by 5 citations

Interaction partners 2. HISTONE H3, : 14 interactors Detail

More details for 14 interactors identified by 10 citations

Experiments performed 4 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18764_4bd3.nef
Input source #2: Coordindates	4bd3.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)
2:6:M3L:N	2:5:VAL:C	unknown	unknown	n/a
2:6:M3L:C	2:7:LYS:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	36	M3L	N-TRIMETHYLLYSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--40-------50--------60--------70--------80--------90-----
SKLTEGQYVLCRWTDGLYYLGKIKRVSSSKQSCLVTFEDNSKYWVLWKDIQHAGVPGE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SKLTEGQYVLCRWTDGLYYLGKIKRVSSSKQSCLVTFEDNSKYWVLWKDIQHAGVPGE
--------10--------20--------30--------40--------50--------

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

--------40-
ATGGVXKPHRY
|||||||||||
ATGGVXKPHRY
--------10-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	58	0	0	100.0
B	B	11	0	0	100.0

Content subtype: combined_18764_4bd3.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	586		100.0 (chain: A, length: 58)
2	Assigned chemical shifts	assigned_chem_shift_list_1_2	Warning	52		13.8 (chain: A, length: 58), 90.9 (chain: B, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2065 (1)	noe	100.0 (chain: A, length: 58), 81.8 (chain: B, length: 11)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	40 (1)	hbond	44.8 (chain: A, length: 58)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	98 (98)	.	94.8 (chain: A, length: 58)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 329
  - ¹³C chemical shifts: 198
  - ¹⁵N chemical shifts: 59
- 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
Saveframe: assigned_chem_shift_list_1_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 13.8%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 90.9%
- Total number of assignments
  - ¹H chemical shifts: 52
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
89	HIS	HE2	7.595

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	365	328	89.9
¹³C chemical shifts	274	198	72.3
¹⁵N chemical shifts	66	59	89.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	120	116	96.7
¹³C chemical shifts	116	56	48.3
¹⁵N chemical shifts	57	54	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	245	212	86.5
¹³C chemical shifts	158	142	89.9
¹⁵N chemical shifts	9	5	55.6

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	27	65.9
¹³C chemical shifts	38	24	63.2
¹⁵N chemical shifts	3	1	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	31	43.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	3	13.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	28	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	3	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	3	50.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 81.8%
- Total number of restraints: 2060
- Weight of restraints: 1.0 (2060)
- Potential type of restraints: square-well-parabolic (2060)
- Range of distance target values: 1.75, 4.0 (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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 44.8%
  - Total number of restraints: 40
  - Weight of restraints: 1.0 (40)
  - Potential type of restraints: square-well-parabolic (40)
  - Range of distance target values: 2.05, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 94.8%
- Total number of restraints: 98
- Total number of restraints per polymer type: 98
- Weight of restraints: 1.0 (98)
- Potential type of restraints: square-well-parabolic (98)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords H3K36ME3, HISTONE RECOGNITION, PHF-19, TRANSCRIPTION, Tudor domain

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Found 1 Document (1.23 seconds)

BMRB: 18764

Sample

Sample

Entries sharing articles Swiss-Prot: 5 entries Detail

Related entities 1. PHD FINGER PROTEIN 19, : 2 : 22 entities Detail

Related entities 2. HISTONE H3, : 39 : 28 entities Detail

Interaction partners 1. PHD FINGER PROTEIN 19, : 15 interactors Detail

Interaction partners 2. HISTONE H3, : 14 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail