BMRBj - BMREntryMaster

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BMRB: 34527

6ZOP

Structure of the cysteine-rich domain of PiggyMac, a domesticated PiggyBac transposase involved in programmed genome rearrangements

Authors

Bessa, L., Guerineau, M., Moriau, S., Lescop, E., Bontems, F., Mathy, N., Guittet, E., Bischerour, J., Betermier, M., Morellet, N.

Assembly

DDE Tnp 1 7 domain-containing protein

Entity

1. DDE Tnp 1 7 domain-containing protein, entity 1 (polymer, Thiol state: all other bound), 84 monomers, 9657.959 Da Detail

GPLGSPEFSY FAKIQPHTFI EGEEIVKCSE CGNETKVFCQ ECTILKAEVV GLCHEKDTIK CQRFHEFMDF ELDKNKEVID KRKG

2. DDE Tnp 1 7 domain-containing protein, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

9788.777 Da

Max. entity weight

9657.959 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS17:ND1	2:ZN1:ZN
2	na	sing	1:HIS65:NE2	2:ZN1:ZN
3	na	sing	1:CYS39:SG	2:ZN1:ZN
4	na	sing	1:CYS42:SG	2:ZN1:ZN
5	na	sing	1:CYS28:SG	2:ZN1:ZN
6	na	sing	1:CYS31:SG	2:ZN1:ZN
7	na	sing	1:CYS53:SG	2:ZN1:ZN
8	na	sing	1:CYS61:SG	2:ZN1:ZN

Source organism

Paramecium tetraurelia

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 84.2 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.2 % (850 of 1010)	80.9 % (429 of 530)	87.5 % (343 of 392)	88.6 % (78 of 88)
Backbone	95.6 % (476 of 498)	92.4 % (158 of 171)	97.6 % (240 of 246)	96.3 % (78 of 81)
Sidechain	76.1 % (449 of 590)	75.5 % (271 of 359)	79.5 % (178 of 224)	0.0 % (0 of 7)
Aromatic	57.8 % (52 of 90)	86.7 % (39 of 45)	28.9 % (13 of 45)
Methyl	87.5 % (63 of 72)	88.9 % (32 of 36)	86.1 % (31 of 36)

1. entity 1

GPLGSPEFSY FAKIQPHTFI EGEEIVKCSE CGNETKVFCQ ECTILKAEVV GLCHEKDTIK CQRFHEFMDF ELDKNKEVID KRKG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

Release date

2020-07-29

Citation

The unusual structure of the PiggyMac cysteine-rich domain reveals zinc finger diversity in PiggyBac-related transposases
Guerineau, M., Bessa, L., Moriau, S., Lescop, E., Bontems, F., Mathy, N., Guittet, E., Bischerour, J., Betermier, M., Morellet, N.
Mob. DNA (2021), 12, 12-12, PubMed 33926516 , DOI 10.1186/s13100-021-00240-4 , Abstract

Related entities 1. DDE Tnp 1 7 domain-containing protein, entity 1, : 1 entities Detail

Experiments performed 10 experiments Detail

1 3D HNCO

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

2 3D HNCACO

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

3 3D HNCA

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

4 3D HN(CO)CA

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

5 3D HNCACB

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

6 3D HN(COCA)CB

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

7 3D HCCH-TOCSY

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

8 3D HCCCONH

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

9 3D 1H-15N NOESY

Instrument

Bruker AVANCE III HD - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

10 3D 1H-13C NOESY

Instrument

Bruker AVANCE III HD - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 293 (±0.1) K, pH 6.8 (±0.05), Details 400 uM U-15N U-13C cysteine-rich domain of PiggyMac, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	cysteine-rich domain of PiggyMac	[U-15N; U-13C]		400 (±1.0) uM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34527_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	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)
1:17:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:65:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:39:CYS:SG	2:1:ZN:ZN	reduced, CA 58.164, CB 29.878 ppm	unknown	n/a
1:42:CYS:SG	2:1:ZN:ZN	reduced, CA 65.56, CB 28.238 ppm	unknown	n/a
1:28:CYS:SG	3:1:ZN:ZN	reduced, CA 60.256, CB 29.927 ppm	unknown	n/a
1:31:CYS:SG	3:1:ZN:ZN	oxidized 30.7%, reduced 69.3%, CA 58.857, CB 33.098 ppm	unknown	n/a
1:53:CYS:SG	3:1:ZN:ZN	reduced, CA 64.951, CB 30.74 ppm	unknown	n/a
1:61:CYS:SG	3:1:ZN:ZN	reduced, CA 64.352, CB 29.104 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr34527_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	918		98.8 (chain: 1, length: 84)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 84, Sequence coverage: 98.8%
- Total number of assignments
  - ¹³C chemical shifts: 343
  - ¹H chemical shifts: 497
  - ¹⁵N chemical shifts: 78
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords GENE REGULATION, cysteine-riche domain, piggyMac, transposase, zinc-finger