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BMRB: 18813

2M0O

The solution structure of human PHF1 in complex with H3K36me3

Authors

Song, J., Patel, D.J.

Assembly

human PHF1 in complex with H3K36me3

Entity

1. human PHF1 in complex with H3K36me3, entity 1 (polymer, Thiol state: not reported), 79 monomers, 8728.773 Da Detail

SRLSRSGASS LWDPASPAPT SGPRPRLWEG QDVLARWTDG LLYLGTIKKV DSAREVCLVQ FEDDSQFLVL WKDISPAAL

2. human PHF1 in complex with H3K36me3, entity 2 (polymer, Thiol state: not present), 11 monomers, 1256.475 Da Detail

ATGGVXKPHR Y

Total weight

9985.248 Da

Max. entity weight

8728.773 Da

Source organism

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.8 %, Completeness: 68.0 %, Completeness (bb): 76.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	68.0 % (692 of 1018)	70.6 % (373 of 528)	64.1 % (257 of 401)	69.7 % (62 of 89)
Backbone	76.2 % (396 of 520)	82.6 % (147 of 178)	72.3 % (188 of 260)	74.4 % (61 of 82)
Sidechain	62.1 % (360 of 580)	64.6 % (226 of 350)	59.6 % (133 of 223)	14.3 % (1 of 7)
Aromatic	37.5 % (33 of 88)	47.7 % (21 of 44)	27.5 % (11 of 40)	25.0 % (1 of 4)
Methyl	78.0 % (78 of 100)	80.0 % (40 of 50)	76.0 % (38 of 50)

1. entity 1

SRLSRSGASS LWDPASPAPT SGPRPRLWEG QDVLARWTDG LLYLGTIKKV DSAREVCLVQ FEDDSQFLVL WKDISPAAL

2. entity 2

ATGGVXKPHR Y

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M0O, Strand ID: A, B Detail

Release date

2012-01-14

Citation

An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting
Cai, L., Rothbart, S.B., Lu, R., Xu, B., Chen, W., Tripathy, A., Rockowitz, S., Zheng, D., Patel, D.J., Allis, C., Strahl, B.D., Song, J., Wang, G.
Mol. Cell (2013), 49, 571-582, PubMed 23273982 , DOI 10.1016/j.molcel.2012.11.026 , Abstract

Related entities 1. human PHF1 in complex with H3K36me3, entity 1, : 5 : 3 entities Detail

Related entities 2. human PHF1 in complex with H3K36me3, entity 2, : 39 : 28 entities Detail

Interaction partners 1. human PHF1 in complex with H3K36me3, entity 1, : 27 interactors Detail

More details for 27 interactors identified by 10 citations

Interaction partners 2. human PHF1 in complex with H3K36me3, entity 2, : 14 interactors Detail

More details for 14 interactors identified by 10 citations

Experiments performed 9 experiments Detail

1 3D 1H-13C NOESY aliphatic

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

2 3D 1H-13C NOESY aromatic

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

3 2D 1H-15N HSQC

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

4 3D HNCACB

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

5 3D HBHA(CO)NH

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

6 3D CBCA(CO)NH

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

7 3D HCCH-TOCSY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

8 2D 1H-1H NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

9 3D 1H-15N NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	human PHF1	[U-100% 13C; U-100% 15N]		0.3 ~ 0.5 mM
2	H3K36me3	natural abundance		0.6 ~ 1.0 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18813_2m0o.nef
Input source #2: Coordindates	2m0o.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)
2:5:VAL:C	2:6:M3L:N	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	336	M3L	N-TRIMETHYLLYSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

----10--------20--------30--------40--------50--------60--------70--------80---
SRLSRSGASSLWDPASPAPTSGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAAL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SRLSRSGASSLWDPASPAPTSGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAAL
--------10--------20--------30--------40--------50--------60--------70---------

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

-------340-
ATGGVXKPHRY
|||||||||||
ATGGVXKPHRY
--------10-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0
B	B	11	0	0	100.0

Content subtype: combined_18813_2m0o.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	660		87.3 (chain: A, length: 79), 90.9 (chain: B, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1058 (1)	noe	86.1 (chain: A, length: 79), 81.8 (chain: B, length: 11)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	32 (1)	hbond	26.6 (chain: A, length: 79), 9.1 (chain: B, length: 11)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	96 (96)	.	75.9 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 87.3%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 90.9%
- Total number of assignments
  - ¹H chemical shifts: 360
  - ¹³C chemical shifts: 239
  - ¹⁵N chemical shifts: 61
- 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

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: 79, Sequence coverage: 86.1%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 81.8%
- Total number of restraints: 1058
- Weight of restraints: 1.0 (1058)
- Potential type of restraints: square-well-parabolic (1058)
- Range of distance target values: 2.4, 3.75 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 26.6%
    - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 9.1%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: square-well-parabolic (32)
  - Range of distance target values: 2.1, 2.6 (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: 79, Sequence coverage: 75.9%
- Total number of restraints: 96
- Total number of restraints per polymer type: 96
- Weight of restraints: 1.0 (96)
- Potential type of restraints: square-well-parabolic (96)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords H3K36me3 binding, Tudor Domain