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BMRB: 15671

2K17

Solution structure of the TAF3 PHD domain in complex with a H3K4me3 peptide

Authors

van Ingen, H., van Schaik, F.M.A., Wienk, H., Timmers, M., Boelens, R.

Assembly

TAF3-PHD finger

Entity

1. TAF3 PHD (polymer, Thiol state: all other bound), 75 monomers, 8600.841 Da Detail

GSHMAMAYVI RDEWGNQIWI CPGCNKPDDG SPMIGCDDCD DWYHWPCVGI MAAPPEEMQW FCPKCANKIK KDKKH

2. ZN (non-polymer), 65.409 × 2 Da
3. H3K4me3 (polymer, Thiol state: not present), 13 monomers, 1404.595 Da Detail

ARTXQTARKS TGG

Total weight

10136.254 Da

Max. entity weight

8600.841 Da

Source organism

Mus musculus , Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 82.9 %, Completeness (bb): 77.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.9 % (827 of 998)	95.4 % (501 of 525)	65.7 % (251 of 382)	82.4 % (75 of 91)
Backbone	77.6 % (394 of 508)	97.1 % (170 of 175)	62.8 % (159 of 253)	81.3 % (65 of 80)
Sidechain	88.2 % (502 of 569)	94.6 % (331 of 350)	77.4 % (161 of 208)	90.9 % (10 of 11)
Aromatic	90.8 % (89 of 98)	100.0 % (49 of 49)	79.5 % (35 of 44)	100.0 % (5 of 5)
Methyl	90.4 % (47 of 52)	100.0 % (26 of 26)	80.8 % (21 of 26)

1. TAF3 PHD

GSHMAMAYVI RDEWGNQIWI CPGCNKPDDG SPMIGCDDCD DWYHWPCVGI MAAPPEEMQW FCPKCANKIK KDKKH

3. H3K4me3

ARTXQTARKS TGG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	TAF3_PHD	[U-13C; U-15N]	0.4 mM
2	H3K4me3	[U-13C; U-15N]	0.4 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	20 mM
5	ZnCl2	natural abundance	0.01 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2K17, Strand ID: A, P Detail

Release date

2008-08-21

Citation

Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3
van Ingen, H., van Schaik, F.M.A., Wienk, H., Ballering, J., Rehmann, H., Deschesne, A.C., Kruijzer, J.A.W., Liskamp, R.M.J., Timmers, H., Boelens, R.
Structure (2008), 16, 1245-1256, PubMed 18682226 , DOI 10.1016/j.str.2008.04.015 , Abstract

Related entities 1. TAF3 PHD, : 1 : 1 : 2 : 42 entities Detail

Related entities 3. H3K4me3, : 98 entities Detail

Interaction partners 1. TAF3 PHD, : 6 interactors Detail

More details for 6 interactors identified by 4 citations

Interaction partners 3. H3K4me3, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15671_2k17.nef
Input source #2: Coordindates	2k17.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)
2:21:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:24:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:36:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:39:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:44:HIS:ND1	3:2:ZN:ZN	unknown	unknown	n/a
2:47:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:62:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:65:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:3:THR:C	1:4:M3L:N	unknown	unknown	n/a
1:4:M3L:C	1:5:GLN:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None
P	4	M3L	N-TRIMETHYLLYSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
P	P	13	0	0	100.0
A	A	75	0	0	100.0

Content subtype: combined_15671_2k17.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	829		100.0 (chain: A, length: 75), 100.0 (chain: P, length: 13)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1866 (1)	noe	94.7 (chain: A, length: 75), 92.3 (chain: P, length: 13)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	67 (67)	.	66.7 (chain: A, length: 75), 23.1 (chain: P, length: 13)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 100.0%
  - Entity_assembly_ID: P, Chain length: 13, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 517
  - ¹³C chemical shifts: 236
  - ¹⁵N chemical shifts: 76
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: P
- 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: A
  - Chain_ID: P

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
893	HIS	HE2	10.577
893	HIS	ND1	164.391

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	461	439	95.2
¹³C chemical shifts	337	236	70.0
¹⁵N chemical shifts	79	75	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	146	98.0
¹³C chemical shifts	150	75	50.0
¹⁵N chemical shifts	68	65	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	293	93.9
¹³C chemical shifts	187	161	86.1
¹⁵N chemical shifts	11	10	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	22	84.6
¹³C chemical shifts	26	22	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	49	100.0
¹³C chemical shifts	44	35	79.5
¹⁵N chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	76	98.7
¹³C chemical shifts	45	0	0.0
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	27	96.4
¹³C chemical shifts	24	0	0.0
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	49	100.0
¹³C chemical shifts	21	0	0.0
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0
¹³C chemical shifts	8	0	0.0

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: 75, Sequence coverage: 94.7%
  - Entity_assembly_ID: P, Chain length: 13, Sequence coverage: 92.3%
- Total number of restraints: 1866
- Weight of restraints: 1.0 (1866)
- Potential type of restraints: square-well-parabolic (1866)
- Range of distance target values: 1.36, 4.2 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: P
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 66.7%
  - Entity_assembly_ID: P, Chain length: 13, Sequence coverage: 23.1%
- Total number of restraints: 67
- Total number of restraints per polymer type: 67
- Weight of restraints: 1.0 (67)
- Potential type of restraints: square-well-parabolic (67)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords histone modifications, NMR, PHD, TFIID, PROTEIN

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Found 1 Document (1.48 seconds)

BMRB: 15671

Sample

Related entities 1. TAF3 PHD, : 1 : 1 : 2 : 42 entities Detail

Related entities 3. H3K4me3, : 98 entities Detail

Interaction partners 1. TAF3 PHD, : 6 interactors Detail

Interaction partners 3. H3K4me3, : 2 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail