BMRBj - BMREntryMaster

Found 1 Document (0.944 seconds)

BMRB: 34061

5M9Z

Second zinc-binding domain from yeast Pcf11

Authors

Mackereth, C.

Assembly

Protein PCF11

Entity

1. Protein PCF11 (polymer), 97 monomers, 10824.87 Da Detail

GSVDNTLGSD RSNELEIRGK YVVVPETSQD MAFKCPICKE TVTGVYDEES GEWVWKNTIE VNGKYFHSTC YHETSQNSSK SNSGKVGLDD LKKLVTK

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

Total weight

10890.279 Da

Max. entity weight

10824.87 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 60.8 %, Completeness: 56.6 %, Completeness (bb): 55.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	56.6 % (624 of 1103)	57.2 % (327 of 572)	56.3 % (240 of 426)	54.3 % (57 of 105)
Backbone	55.9 % (323 of 578)	56.0 % (112 of 200)	55.8 % (158 of 283)	55.8 % (53 of 95)
Sidechain	57.5 % (353 of 614)	57.8 % (215 of 372)	57.8 % (134 of 232)	40.0 % (4 of 10)
Aromatic	88.1 % (74 of 84)	100.0 % (42 of 42)	75.0 % (30 of 40)	100.0 % (2 of 2)
Methyl	57.8 % (52 of 90)	60.0 % (27 of 45)	55.6 % (25 of 45)

1. Protein PCF11

GSVDNTLGSD RSNELEIRGK YVVVPETSQD MAFKCPICKE TVTGVYDEES GEWVWKNTIE VNGKYFHSTC YHETSQNSSK SNSGKVGLDD LKKLVTK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 360 uM Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Pcf11	natural abundance	360 uM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	zinc acetate	natural abundance	50 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	Pcf11	[U-99% 15N]	250 uM
8	TRIS	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	zinc acetate	natural abundance	50 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 230 uM [U-99% 13C; U-99% 15N] Pcf11, 50 mM na TRIS, 150 mM na sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
14	TRIS	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	zinc acetate	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 230 uM [U-99% 13C; U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 100% D2O

#	Name	Isotope labeling	Concentration
19	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
20	TRIS	natural abundance	50 mM
21	sodium chloride	natural abundance	150 mM
22	zinc acetate	natural abundance	50 uM
23	D2O	natural abundance	100 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 100 uM [U-10% 13C; U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
24	Pcf11	[U-10% 13C; U-99% 15N]	100 uM
25	TRIS	natural abundance	50 mM
26	sodium chloride	natural abundance	150 mM
27	zinc acetate	natural abundance	50 uM
28	H2O	natural abundance	90 %
29	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.37 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.37 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.77 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.32 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 5M9Z, Strand ID: A Detail

Release date

2016-11-10

Citation

Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3'-end processing
Guegueniat, J., Dupin, A.F., Stojko, J., Beaurepaire, L., Cianferani, S., Mackereth, C.D., Minvielle-Sebastia, L., Fribourg, S.
Nucleic Acids Res. (2017), 45, 10115-10131, PubMed 28973460 , DOI 10.1093/nar/gkx674 , Abstract

Related entities 1. Protein PCF11, : 2 : 5 entities Detail

Interaction partners 1. Protein PCF11, : 71 interactors Detail

More details for 71 interactors identified by 6 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avanc - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 250 uM [U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	Pcf11	[U-99% 15N]	250 uM
8	TRIS	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	zinc acetate	natural abundance	50 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

2 3D HNCO

Instrument

Bruker Avanc - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 230 uM [U-99% 13C; U-99% 15N] Pcf11, 50 mM na TRIS, 150 mM na sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
14	TRIS	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	zinc acetate	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

3 3D HNCACO

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
14	TRIS	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	zinc acetate	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

4 3D HNCA

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
14	TRIS	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	zinc acetate	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
14	TRIS	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	zinc acetate	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
14	TRIS	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	zinc acetate	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

7 3D HNHA

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Pcf11	[U-99% 15N]	250 uM
8	TRIS	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	zinc acetate	natural abundance	50 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

8 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 230 uM [U-99% 13C; U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 100% D2O

#	Name	Isotope labeling	Concentration
19	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
20	TRIS	natural abundance	50 mM
21	sodium chloride	natural abundance	150 mM
22	zinc acetate	natural abundance	50 uM
23	D2O	natural abundance	100 %

9 3D H(CCO)NH

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
14	TRIS	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	zinc acetate	natural abundance	50 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

10 3D H(C)CH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
19	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
20	TRIS	natural abundance	50 mM
21	sodium chloride	natural abundance	150 mM
22	zinc acetate	natural abundance	50 uM
23	D2O	natural abundance	100 %

11 3D (H)CCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
19	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
20	TRIS	natural abundance	50 mM
21	sodium chloride	natural abundance	150 mM
22	zinc acetate	natural abundance	50 uM
23	D2O	natural abundance	100 %

12 2D 1H-13C HSQC CT

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 100 uM [U-10% 13C; U-99% 15N] Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
24	Pcf11	[U-10% 13C; U-99% 15N]	100 uM
25	TRIS	natural abundance	50 mM
26	sodium chloride	natural abundance	150 mM
27	zinc acetate	natural abundance	50 uM
28	H2O	natural abundance	90 %
29	D2O	natural abundance	10 %

13 3D 1H-15N NOESY

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Pcf11	[U-99% 15N]	250 uM
8	TRIS	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	zinc acetate	natural abundance	50 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

14 2D 1H-15N HMBC

Instrument

Bruker Avanc - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	Pcf11	[U-99% 15N]	250 uM
8	TRIS	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	zinc acetate	natural abundance	50 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

15 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
19	Pcf11	[U-99% 13C; U-99% 15N]	230 uM
20	TRIS	natural abundance	50 mM
21	sodium chloride	natural abundance	150 mM
22	zinc acetate	natural abundance	50 uM
23	D2O	natural abundance	100 %

16 2D 1H-1H NOESY

Instrument

Bruker Avanc - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 360 uM Pcf11, 50 mM TRIS, 150 mM sodium chloride, 50 uM zinc acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Pcf11	natural abundance	360 uM
2	TRIS	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	zinc acetate	natural abundance	50 uM
5	H2O	natural abundance	90 %
6	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_34061_5m9z.nef
Input source #2: Coordindates	5m9z.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)
1:35:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:38:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:40:GLU:OE2	2:1:ZN:ZN	unknown	unknown	n/a
1:67:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:70: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

530-----540-------550-------560-------570-------580-------590-------600-------610-------620------
GSVDNTLGSDRSNELEIRGKYVVVPETSQDMAFKCPICKETVTGVYDEESGEWVWKNTIEVNGKYFHSTCYHETSQNSSKSNSGKVGLDDLKKLVTK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSVDNTLGSDRSNELEIRGKYVVVPETSQDMAFKCPICKETVTGVYDEESGEWVWKNTIEVNGKYFHSTCYHETSQNSSKSNSGKVGLDDLKKLVTK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	97	0	0	100.0

Content subtype: combined_34061_5m9z.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	581		56.7 (chain: A, length: 97)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1872 (1)	noe	61.9 (chain: A, length: 97)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	134 (134)	.	58.8 (chain: A, length: 97)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 56.7%
- Total number of assignments
  - ¹H chemical shifts: 301
  - ¹³C chemical shifts: 228
  - ¹⁵N chemical shifts: 52
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
601	HIS	ND1	224.041
601	HIS	NE2	167.075

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	572	301	52.6
¹³C chemical shifts	426	228	53.5
¹⁵N chemical shifts	107	50	46.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	200	102	51.0
¹³C chemical shifts	194	102	52.6
¹⁵N chemical shifts	95	47	49.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	372	199	53.5
¹³C chemical shifts	232	126	54.3
¹⁵N chemical shifts	12	3	25.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	26	56.5
¹³C chemical shifts	46	25	54.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	42	100.0
¹³C chemical shifts	40	30	75.0
¹⁵N chemical shifts	2	2	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: 97, Sequence coverage: 61.9%
- Total number of restraints: 1866
- Weight of restraints: 1.0 (1866)
- Potential type of restraints: square-well-parabolic (1866)
- Range of distance target values: 1.75, 4.0 (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: 97, Sequence coverage: 58.8%
- Total number of restraints: 134
- Total number of restraints per polymer type: 134
- Weight of restraints: 1.0 (134)
- Potential type of restraints: square-well-parabolic (134)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords RNA binding protein, RNA processing, mRNA, zinc-binding

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Found 1 Document (0.944 seconds)

BMRB: 34061

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Protein PCF11, : 2 : 5 entities Detail

Interaction partners 1. Protein PCF11, : 71 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail