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BMRB: 50997

Zinc finger

Authors

Overbeck, J., Sprangers, R.

Assembly

zinc finger polypeptide bound to Zn2+

Entity

1. zinc finger polypeptide bound to Zn2+, entity 1 (polymer, Thiol state: all other bound), 31 monomers, 3301.736 Da Detail

GGEAKARLCK LCGQKGHDER SCKGEAKQKQ G

2. zinc finger polypeptide bound to Zn2+, entity ZN (non-polymer), 65.409 Da

Total weight

3367.145 Da

Max. entity weight

3301.736 Da

Source organism

Thermochaetoides thermophila

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 89.0 %, Completeness (bb): 91.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.0 % (308 of 346)	86.1 % (161 of 187)	95.1 % (117 of 123)	83.3 % (30 of 36)
Backbone	91.4 % (170 of 186)	86.8 % (59 of 68)	95.4 % (83 of 87)	90.3 % (28 of 31)
Sidechain	86.5 % (160 of 185)	84.9 % (101 of 119)	95.1 % (58 of 61)	20.0 % (1 of 5)
Aromatic	0.0 % (0 of 4)	0.0 % (0 of 2)	0.0 % (0 of 2)
Methyl	85.7 % (12 of 14)	85.7 % (6 of 7)	85.7 % (6 of 7)

1. entity 1

GGEAKARLCK LCGQKGHDER SCKGEAKQKQ G

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

Release date

2021-06-29

Citation

Observation of conformational changes that underlie the catalytic cycle of Xrn2
Overbeck, J.H., Stelzig, D., Fuchs, A.L., Wurm, J.P., Sprangers, R.
Nat. Chem. Biol. (2022), 18, 1152-1160, PubMed 36008487 , DOI 10.1038/s41589-022-01111-6 , Abstract

Related entities 1. zinc finger polypeptide bound to Zn2+, entity 1, : 47 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

3 3D HNCACB

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

4 3D HN(CA)CO

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

5 3D H(CCO)NH

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

6 3D C(CO)NH

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

7 3D 15N-separated NOESY

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

8 3D 13C-separated NOESY

Instrument

Bruker AVANCE NEO - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	Zinc finger	[U-13C; U-15N]		0.75 mM
2	Zn2+	natural abundance		0.75 mM
3	HEPES	natural abundance		25 mM
4	NaCl	natural abundance		125 mM
5	NaN3	natural abundance		0.03 %

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr50997_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr50997_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	323		93.5 (chain: 1, length: 31)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 31, Sequence coverage: 93.5%
- Total number of assignments
  - ¹H chemical shifts: 176
  - ¹³C chemical shifts: 117
  - ¹⁵N chemical shifts: 30
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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: 1