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BMRB: 30623

6PMG

Solution structure of the C-terminal zinc finger of the C. elegans protein MEX-5

Authors

Massi, F., Tavella, D.

Assembly

Zinc finger protein mex-5

Entity

1. Zinc finger protein mex-5, entity 1 (polymer, Thiol state: all other bound), 35 monomers, 4023.576 Da Detail

NNKYKTKLCK NFARGGTGFC PYGLRCEFVH PTDKE

2. Zinc finger protein mex-5, entity ZN (non-polymer), 65.409 Da

Total weight

4088.9849 Da

Max. entity weight

4023.576 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS9:SG	2:ZN1:ZN
2	na	sing	1:CYS20:SG	2:ZN1:ZN
3	na	sing	1:CYS26:SG	2:ZN1:ZN
4	na	sing	1:HIS30:NE2	2:ZN1:ZN

Source organism

Caenorhabditis elegans

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 94.3 %, Completeness: 83.4 %, Completeness (bb): 76.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.4 % (351 of 421)	90.6 % (202 of 223)	72.2 % (117 of 162)	88.9 % (32 of 36)
Backbone	76.7 % (158 of 206)	90.3 % (65 of 72)	61.4 % (62 of 101)	93.9 % (31 of 33)
Sidechain	90.2 % (222 of 246)	90.7 % (137 of 151)	91.3 % (84 of 92)	33.3 % (1 of 3)
Aromatic	80.0 % (40 of 50)	84.0 % (21 of 25)	76.0 % (19 of 25)
Methyl	100.0 % (20 of 20)	100.0 % (10 of 10)	100.0 % (10 of 10)

1. entity 1

NNKYKTKLCK NFARGGTGFC PYGLRCEFVH PTDKE

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

Protein Blocks Logo

Calculated from 20 models in PDB: 6PMG, Strand ID: X Detail

Release date

2020-01-29

Citation

A Disorder-to-Order Transition Mediates RNA Binding of the Caenorhabditis elegans Protein MEX-5
Tavella, D., Ertekin, A., Schaal, H., Ryder, S.P., Massi, F.
Biophys. J. (2020), 118, 2001-2014, PubMed 32294479 , DOI 10.1016/j.bpj.2020.02.032 , Abstract

Related entities 1. Zinc finger protein mex-5, entity 1, : 1 : 2 : 208 entities Detail

Interaction partners 1. Zinc finger protein mex-5, entity 1, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

3 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

4 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

5 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

6 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

7 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

8 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

12 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

13 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 294 K, pH 6.2, Details 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	MEX-5	[U-13C; U-15N]		300 nM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30623_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	OK

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)
1:9:CYS:SG	2:1:ZN:ZN	reduced, CA 61.427, CB 31.827 ppm	unknown	n/a
1:20:CYS:SG	2:1:ZN:ZN	oxidized 26.8%, reduced 73.2%, CB 32.532 ppm	unknown	n/a
1:26:CYS:SG	2:1:ZN:ZN	reduced, CA 61.627, CB 30.786 ppm	unknown	n/a
1:30:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr30623_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	368		94.3 (chain: 1, length: 35)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 35, Sequence coverage: 94.3%
- Total number of assignments
  - ¹H chemical shifts: 222
  - ¹³C chemical shifts: 114
  - ¹⁵N chemical shifts: 32
- 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 C. elegans, CCCH zinc finger, MEX-5, RNA BINDING PROTEIN, zinc finger protein