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Found 1 Document (0.694 seconds)

BMRB: 25934

2NAB

Nizp1-C2HR zinc finger structure

Authors

Berardi, A., Quilici, G., Spiliotopoulos, D., Corral-Rodriguez, M., Martin, F., Degano, M., Tonon, G., Musco, G.

Assembly

Nizp1-C2HR zinc finger

Entity

1. Nizp1-C2HR zinc finger, entity 1 (polymer), 41 monomers, 4972.739 Da Detail

GAMEVQTSQK SYVCPNCGKI FRWRVNFIRH LRSRREQKPH K

2. ZINC ION (non-polymer), 65.409 Da

Total weight

5038.148 Da

Max. entity weight

4972.739 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.7 %, Completeness: 85.8 %, Completeness (bb): 89.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	85.8 % (279 of 325)	86.1 % (241 of 280)	84.4 % (38 of 45)
Backbone	89.3 % (108 of 121)	87.8 % (72 of 82)	92.3 % (36 of 39)
Sidechain	83.8 % (171 of 204)	85.4 % (169 of 198)	33.3 % (2 of 6)
Aromatic	100.0 % (25 of 25)	100.0 % (24 of 24)	100.0 % (1 of 1)
Methyl	92.9 % (13 of 14)	92.9 % (13 of 14)

1. entity 1

GAMEVQTSQK SYVCPNCGKI FRWRVNFIRH LRSRREQKPH K

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	[U-99% 13C; U-99% 15N]	0.8 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	sodium phosphate	[U-99% 15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	0.8 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
10	sodium phosphate	natural abundance		0.8 mM
11	H2O	natural abundance		100 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2NAB, Strand ID: A Detail

Release date

2016-02-22

Citation

Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome
Berardi, A., Quilici, G., Spiliotopoulos, D., Corral-Rodriguez, M., Martin, F., Degano, M., Tonon, G., Musco, G.
Nucleic Acids Res. (2016), 44, 3448-3463, PubMed 26896805 , DOI 10.1093/nar/gkw103 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25933 released on 2016-07-20
Title NSD1-PHD_5-C5HCH tandem domain structure

Related entities 1. Nizp1-C2HR zinc finger, entity 1, : 1 : 2 : 1612 entities Detail

Interaction partners 1. Nizp1-C2HR zinc finger, entity 1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	sodium phosphate	[U-99% 15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	0.8 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
10	sodium phosphate	natural abundance		0.8 mM
11	H2O	natural abundance		100 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	0.8 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
10	sodium phosphate	natural abundance		0.8 mM
11	H2O	natural abundance		100 %

6 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	[U-99% 13C; U-99% 15N]	0.8 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	[U-99% 13C; U-99% 15N]	0.8 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	sodium phosphate	[U-99% 13C; U-99% 15N]	0.8 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25934_2nab.nef
Input source #2: Coordindates	2nab.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)
1:30:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:17:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:14:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40-
GAMEVQTSQKSYVCPNCGKIFRWRVNFIRHLRSRREQKPHK
|||||||||||||||||||||||||||||||||||||||||
GAMEVQTSQKSYVCPNCGKIFRWRVNFIRHLRSRREQKPHK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	41	0	0	100.0

Content subtype: combined_25934_2nab.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	278		90.2 (chain: A, length: 41)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	799 (1)	noe	90.2 (chain: A, length: 41)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 41, Sequence coverage: 90.2%
- Total number of assignments
  - ¹H chemical shifts: 241
  - ¹⁵N chemical shifts: 37
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	280	241	86.1
¹⁵N chemical shifts	51	37	72.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	72	87.8
¹⁵N chemical shifts	39	35	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	169	85.4
¹⁵N chemical shifts	12	2	16.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	13	86.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	24	100.0
¹⁵N chemical shifts	1	1	100.0

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: 41, Sequence coverage: 90.2%
- Total number of restraints: 794
- Weight of restraints: 1.0 (794)
- Potential type of restraints: square-well-parabolic (794)
- Range of distance target values: 1.81, 5.39 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords C2HR, NSD1, Nizp1, zinc finger

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Found 1 Document (0.694 seconds)

BMRB: 25934

Sample #1

Sample #2

Sample #3

Sample #4

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Nizp1-C2HR zinc finger, entity 1, : 1 : 2 : 1612 entities Detail

Interaction partners 1. Nizp1-C2HR zinc finger, entity 1, : 1 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 3 contents Detail