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Found 1 Document (0.843 seconds)

BMRB: 25953

2NAX

Structure of CCHC zinc finger domain of Pcf11

Authors

Yang, F., Varani, G.

Assembly

CCHC zinc finger domain of Pcf11

Entity

1. CCHC zinc finger domain of Pcf11, entity 1 (polymer), 76 monomers, 8697.282 Da Detail

GGSEFSDRSN ELEIRGKYVV VPETSQDMAF KXPIXKETVT GVYDEESGEW VWKNTIEVNG KYFXSTXYXE TSQNSS

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

Total weight

8762.691 Da

Max. entity weight

8697.282 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.8 %, Completeness: 90.1 %, Completeness (bb): 93.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (737 of 818)	89.9 % (381 of 424)	89.0 % (282 of 317)	96.1 % (74 of 77)
Backbone	93.8 % (396 of 422)	91.1 % (133 of 146)	95.2 % (197 of 207)	95.7 % (66 of 69)
Sidechain	88.1 % (406 of 461)	89.2 % (248 of 278)	85.7 % (150 of 175)	100.0 % (8 of 8)
Aromatic	58.1 % (50 of 86)	72.1 % (31 of 43)	41.5 % (17 of 41)	100.0 % (2 of 2)
Methyl	98.3 % (57 of 58)	96.6 % (28 of 29)	100.0 % (29 of 29)

1. entity 1

GGSEFSDRSN ELEIRGKYVV VPETSQDMAF KXPIXKETVT GVYDEESGEW VWKNTIEVNG KYFXSTXYXE TSQNSS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 15N]	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		1 mM
8	D2O	natural abundance		100 %

Release date

2016-11-16

Citation

The C terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3'-end processing
Yang, F., Hsu, P., Lee, S.D., Yang, W., Hoskinson, D., Xu, W., Moore, C., Varani, G.
RNA (2017), 23, 98-107, PubMed 27780845 , DOI 10.1261/rna.058354.116 , Abstract

Related entities 1. CCHC zinc finger domain of Pcf11, entity 1, : 2 : 2 entities Detail

Interaction partners 1. CCHC zinc finger domain of Pcf11, entity 1, : 71 interactors Detail

More details for 71 interactors identified by 6 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 15N]	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		1 mM
8	D2O	natural abundance		100 %

3 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		1 mM
8	D2O	natural abundance		100 %

9 3D 1H-15N NOESY-HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 15N]	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 3D 1H-13C NOESY-HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]		1 mM
8	D2O	natural abundance		100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25953_2nax.nef
Input source #2: Coordindates	2nax.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	Error

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)
1:64:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:35:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:32:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:67: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

-----540-------550-------560-------570-------580-------590-------600--------
GGSEFSDRSNELEIRGKYVVVPETSQDMAFKCPICKETVTGVYDEESGEWVWKNTIEVNGKYFHSTCYHETSQNSS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGSEFSDRSNELEIRGKYVVVPETSQDMAFKCPICKETVTGVYDEESGEWVWKNTIEVNGKYFHSTCYHETSQNSS
--------10--------20--------30--------40--------50--------60--------70------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_25953_2nax.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	Error	770		89.5 (chain: A, length: 76)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	907 (1)	noe	85.5 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 89.5%
- Total number of assignments
  - ¹H chemical shifts: 396
  - ¹³C chemical shifts: 291
  - ¹⁵N chemical shifts: 77
  - ¹⁷O chemical shifts: 6
- Completeness of assignments
- Peptide bond of PRO
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 85.5%
- Total number of restraints: 907
- Weight of restraints: 1.0 (907)
- Potential type of restraints: upper-bound-parabolic (907)
- Range of distance target values: 2.63, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords zinc finger

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Found 1 Document (0.843 seconds)

BMRB: 25953

Sample #1

Sample #2

Sample #3

Related entities 1. CCHC zinc finger domain of Pcf11, entity 1, : 2 : 2 entities Detail

Interaction partners 1. CCHC zinc finger domain of Pcf11, entity 1, : 71 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail