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BMRB: 16397

2KKR

Solution structure of SCA7 zinc finger domain from human ataxin-7 protein

Authors

Wang, Y., Atkinson, A.R., Bonnet, J., Romier, C., Kieffer, B.

Assembly

human ataxin-7

Entity

1. SCA7 domain (polymer, Thiol state: all other bound), 74 monomers, 8742.994 Da Detail

GSKFLNKRLS EREFDPDIHC GVIDLDTKKP CTRSLTCKTH SLTQRRAVQG RRKRFDVLLA EHKNKTREKE LIRH

2. ZN (non-polymer), 65.409 Da

Total weight

8808.403 Da

Max. entity weight

8742.994 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 95.4 %, Completeness (bb): 95.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	95.4 % (460 of 482)	95.4 % (460 of 482)
Backbone	95.3 % (142 of 149)	95.3 % (142 of 149)
Sidechain	95.5 % (318 of 333)	95.5 % (318 of 333)
Aromatic	95.7 % (22 of 23)	95.7 % (22 of 23)
Methyl	100.0 % (36 of 36)	100.0 % (36 of 36)

1. SCA7 domain

GSKFLNKRLS EREFDPDIHC GVIDLDTKKP CTRSLTCKTH SLTQRRAVQG RRKRFDVLLA EHKNKTREKE LIRH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		200 mM
3	DTT	natural abundance		2 mM
4	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		200 mM
9	DTT	natural abundance		2 mM
10	entity_1	natural abundance		0.6 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2010-10-17

Citation

The structural plasticity of SCA7 domains defines their differential nucleosome-binding properties
Bonnet, J., Wang, Y., Spedale, G., Atkinson, R., Romier, C., Hamiche, A., Pijnappel, W., Timmers, H., Tora, L., Devys, D., Kieffer, B.
EMBO Rep. (2010), 11, 612-618, PubMed 20634802 , DOI 10.1038/embor.2010.98 , Abstract

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 16402 released on 2010-10-17
    Title Solution structure of SCA7 zinc finger domain from human Ataxin-7-L3 protein
  Swiss-Prot: Q14CW9 released on 2007-02-20
    Title AT7L3_HUMAN Entity Ataxin-7-like protein 3

Related entities 1. SCA7 domain, : 1 : 4 : 13 entities Detail

Interaction partners 1. SCA7 domain, : 55 interactors Detail

More details for 55 interactors identified by 5 citations

Experiments performed 8 experiments Detail

1 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		200 mM
3	DTT	natural abundance		2 mM
4	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		200 mM
3	DTT	natural abundance		2 mM
4	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		200 mM
3	DTT	natural abundance		2 mM
4	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		200 mM
3	DTT	natural abundance		2 mM
4	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HN(CO)CACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		200 mM
3	DTT	natural abundance		2 mM
4	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	sodium chloride	natural abundance		200 mM
3	DTT	natural abundance		2 mM
4	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		200 mM
9	DTT	natural abundance		2 mM
10	entity_1	natural abundance		0.6 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

8 2D 1H-1H TOCSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.4) K, pH 7.1 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		200 mM
9	DTT	natural abundance		2 mM
10	entity_1	natural abundance		0.6 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16397_2kkr.nef
Input source #2: Coordindates	2kkr.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)
1:20:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:31:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:37:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:40:HIS:ND1	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

--330-----340-------350-------360-------370-------380-------390-------400-
GSKFLNKRLSEREFDPDIHCGVIDLDTKKPCTRSLTCKTHSLTQRRAVQGRRKRFDVLLAEHKNKTREKELIRH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKFLNKRLSEREFDPDIHCGVIDLDTKKPCTRSLTCKTHSLTQRRAVQGRRKRFDVLLAEHKNKTREKELIRH
--------10--------20--------30--------40--------50--------60--------70----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	74	0	0	100.0

Content subtype: combined_16397_2kkr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	468		97.3 (chain: A, length: 74)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1848 (1)	noe	97.3 (chain: A, length: 74)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	56 (56)	.	56.8 (chain: A, length: 74)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 468
- 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

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: 74, Sequence coverage: 97.3%
- Total number of restraints: 1838
- Weight of restraints: 1.0 (1838)
- Potential type of restraints: square-well-parabolic (1838)
- Range of distance target values: 2.1, 3.65 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 56.8%
- Total number of restraints: 56
- Total number of restraints per polymer type: 56
- Weight of restraints: 1.0 (56)
- Potential type of restraints: square-well-parabolic (56)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords transcription, Zinc Finger