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BMRB: 30030

5IJ4

Solution structure of AN1-type zinc finger domain from Cuz1 (Cdc48 associated ubiquitin-like/zinc-finger protein-1)

Authors

Sun, Z.J., Hanna, J., Wagner, G., Bhanu, M.K., Allan, M., Arthanari, H.

Assembly

CDC48-associated ubiquitin-like/zinc finger protein 1

Entity

1. CDC48-associated ubiquitin-like/zinc finger protein 1 (polymer), 49 monomers, 5992.740 Da Detail

MLDVGKHCAY CRQLDFLPFH CSFCNEDFCS NHRLKEDHHC RWLLEHEEV

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

Total weight

6123.558 Da

Max. entity weight

5992.74 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.1 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.1 % (573 of 590)	98.4 % (302 of 307)	94.8 % (219 of 231)	100.0 % (52 of 52)
Backbone	100.0 % (292 of 292)	100.0 % (98 of 98)	100.0 % (146 of 146)	100.0 % (48 of 48)
Sidechain	95.1 % (329 of 346)	97.6 % (204 of 209)	91.0 % (121 of 133)	100.0 % (4 of 4)
Aromatic	86.9 % (73 of 84)	97.6 % (41 of 42)	75.6 % (31 of 41)	100.0 % (1 of 1)
Methyl	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)

1. CDC48-associated ubiquitin-like/zinc finger protein 1

MLDVGKHCAY CRQLDFLPFH CSFCNEDFCS NHRLKEDHHC RWLLEHEEV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.0 mM [U-100% 15N] cuz1, 5 mM Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	NaCl	natural abundance	50 mM
3	Tris	natural abundance	5 mM
4	ZnCl2	natural abundance	0.2 mM
5	cuz1	[U-100% 15N]	1.0 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.7 mM [U-100% 13C; U-100% 15N] cuz1, 5 mM Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.85 mM cuz1, 5 mM [U-2H] Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
15	DTT	[U-2H]	1 mM
16	NaCl	natural abundance	50 mM
17	Tris	[U-2H]	5 mM
18	ZnCl2	natural abundance	0.2 mM
19	cuz1	natural abundance	0.85 mM
20	D2O	natural abundance	100 %

LACS Plot; CA

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

Referencing offset: -0.38 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.38 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.13 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.52 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 5IJ4, Strand ID: A Detail

Release date

2016-09-29

Citation

Solution Structure of the Cuz1 AN1 Zinc Finger Domain: An Exposed LDFLP Motif Defines a Subfamily of AN1 Proteins
Sun, Z.J., Bhanu, M.K., Allan, M., Arthanari, H., Wagner, G., Hanna, J.
PLoS One (2016), 11, e0163660-e0163660, PubMed 27662200 , DOI 10.1371/journal.pone.0163660 , Abstract

Related entities 1. CDC48-associated ubiquitin-like/zinc finger protein 1, : 1 : 2 : 50 entities Detail

Interaction partners 1. CDC48-associated ubiquitin-like/zinc finger protein 1, : 12 interactors Detail

More details for 12 interactors identified by 4 citations

Experiments performed 16 experiments Detail

1 3D 1H-15N NOESY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.0 mM [U-100% 15N] cuz1, 5 mM Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	NaCl	natural abundance	50 mM
3	Tris	natural abundance	5 mM
4	ZnCl2	natural abundance	0.2 mM
5	cuz1	[U-100% 15N]	1.0 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D 1H-13C NOESY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.7 mM [U-100% 13C; U-100% 15N] cuz1, 5 mM Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

3 3D HNCA

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

4 3D HN(CO)CA

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

6 3D HN(CA)CO

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

7 3D HNCACB

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

8 3D HN(COCA)CB

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

9 3D C(CO)NH

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

10 3D H(CCO)NH

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

11 3D HCCH-TOCSY

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

12 2D NOESY

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.85 mM cuz1, 5 mM [U-2H] Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
15	DTT	[U-2H]	1 mM
16	NaCl	natural abundance	50 mM
17	Tris	[U-2H]	5 mM
18	ZnCl2	natural abundance	0.2 mM
19	cuz1	natural abundance	0.85 mM
20	D2O	natural abundance	100 %

13 2D TOCSY

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.85 mM cuz1, 5 mM [U-2H] Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM [U-2H] DTT, 100% D2O

#	Name	Isotope labeling	Concentration
15	DTT	[U-2H]	1 mM
16	NaCl	natural abundance	50 mM
17	Tris	[U-2H]	5 mM
18	ZnCl2	natural abundance	0.2 mM
19	cuz1	natural abundance	0.85 mM
20	D2O	natural abundance	100 %

14 2D 1H-15N HSQC

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

15 2D 1H-13C HSQC

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

16 2D 1H-13C HSQC aromatic

Instrument

Agilent DD2 - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
8	DTT	natural abundance	1 mM
9	NaCl	natural abundance	50 mM
10	Tris	natural abundance	5 mM
11	ZnCl2	natural abundance	0.2 mM
12	cuz1	[U-100% 13C; U-100% 15N]	0.7 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30030_5ij4.nef
Input source #2: Coordindates	5ij4.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)
1:8:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:11:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:21:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:24:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:29:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:32:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:38:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a
1:40:CYS:SG	2:2: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	Distance restraints
B	2	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------20--------30--------40--------50---------
MLDVGKHCAYCRQLDFLPFHCSFCNEDFCSNHRLKEDHHCRWLLEHEEV
|||||||||||||||||||||||||||||||||||||||||||||||||
MLDVGKHCAYCRQLDFLPFHCSFCNEDFCSNHRLKEDHHCRWLLEHEEV
--------10--------20--------30--------40---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	49	0	0	100.0

Content subtype: combined_30030_5ij4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	584		100.0 (chain: A, length: 49)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Error	60 (1)	undefined	16.3 (chain: A, length: 49), 50.0 (chain: B, length: 2)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	875 (1)	noe	100.0 (chain: A, length: 49)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	63 (63)	.	83.7 (chain: A, length: 49)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 100.0%

--------20--------30--------40--------50---------
MLDVGKHCAYCRQLDFLPFHCSFCNEDFCSNHRLKEDHHCRWLLEHEEV
|||||||||||||||||||||||||||||||||||||||||||||||||
MLDVGKHCAYCRQLDFLPFHCSFCNEDFCSNHRLKEDHHCRWLLEHEEV

Total number of assignments
- ¹H chemical shifts: 303
- ¹³C chemical shifts: 219
- ¹⁵N chemical shifts: 62

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
30	HIS	ND1	178.714
30	HIS	NE2	179.503
42	HIS	ND1	217.721
42	HIS	NE2	172.002
48	HIS	HD1	10.436
48	HIS	ND1	175.806
48	HIS	NE2	215.747
49	HIS	ND1	186.373
49	HIS	NE2	177.845
56	HIS	ND1	192.381
56	HIS	NE2	176.266

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	307	302	98.4
¹³C chemical shifts	231	219	94.8
¹⁵N chemical shifts	55	52	94.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	98	100.0
¹³C chemical shifts	98	98	100.0
¹⁵N chemical shifts	48	48	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	209	204	97.6
¹³C chemical shifts	133	121	91.0
¹⁵N chemical shifts	7	4	57.1

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	17	94.4
¹³C chemical shifts	18	17	94.4

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	41	97.6
¹³C chemical shifts	41	31	75.6
¹⁵N chemical shifts	1	1	100.0

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Error
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 16.3%
  - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
- Total number of restraints: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: upper-bound-parabolic (60)
- Range of distance target values: 2.14, 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
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 100.0%
  - Total number of restraints: 875
  - Weight of restraints: 1.0 (875)
  - Potential type of restraints: upper-bound-parabolic (875)
  - Range of distance target values: 2.3, 9.73 (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: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 83.7%
- Total number of restraints: 63
- Total number of restraints per polymer type: 63
- Weight of restraints: 1.0 (63)
- Potential type of restraints: square-well-parabolic (63)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords METAL BINDING PROTEIN

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Found 1 Document (0.703 seconds)

BMRB: 30030

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CDC48-associated ubiquitin-like/zinc finger protein 1, : 1 : 2 : 50 entities Detail

Interaction partners 1. CDC48-associated ubiquitin-like/zinc finger protein 1, : 12 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 5 contents Detail