BMRBj - BMREntryMaster

Found 1 Document (1.171 seconds)

BMRB: 15074

2JMO

Assignment of the 1H, 15N and 13C resonances and determination of the 3D- structure of In-Between-RING (IBR) domain of Parkin

Authors

Shaw, G.S., Beasley, S.A.

Assembly

IBR domain of Parkin

Entity

1. IBR domain of human Parkin (polymer, Thiol state: free and other bound), 80 monomers, 8610.536 Da Detail

GHMGEEQYNR YQQYGAEECV LQMGGVLCPR PGCGAGLLPE PDQRKVTCEG GNGLGCGFAF CRECKEAYHE GECSAVFEAS

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

8741.3545 Da

Max. entity weight

8610.536 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS28:SG	2:ZN1:ZN
2	na	sing	1:CYS33:SG	2:ZN1:ZN
3	na	sing	1:CYS48:SG	2:ZN1:ZN
4	na	sing	1:CYS56:SG	2:ZN1:ZN
5	na	sing	1:CYS61:SG	2:ZN1:ZN
6	na	sing	1:CYS64:SG	2:ZN1:ZN
7	na	sing	1:CYS73:SG	2:ZN1:ZN
8	na	sing	1:HIS69:NE2	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.4 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.4 % (795 of 860)	94.0 % (423 of 450)	89.0 % (291 of 327)	97.6 % (81 of 83)
Backbone	96.2 % (454 of 472)	97.6 % (166 of 170)	94.7 % (214 of 226)	97.4 % (74 of 76)
Sidechain	89.6 % (407 of 454)	91.8 % (257 of 280)	85.6 % (143 of 167)	100.0 % (7 of 7)
Aromatic	65.7 % (46 of 70)	85.7 % (30 of 35)	45.7 % (16 of 35)
Methyl	98.0 % (49 of 50)	100.0 % (25 of 25)	96.0 % (24 of 25)

1. IBR domain of human Parkin

GHMGEEQYNR YQQYGAEECV LQMGGVLCPR PGCGAGLLPE PDQRKVTCEG GNGLGCGFAF CRECKEAYHE GECSAVFEAS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

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: -0.12 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: -0.12 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: 0.04 ppm, Outliers: 3 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 20 models in PDB: 2JMO, Strand ID: A Detail

Release date

2007-05-08

Citation

Structure of the Parkin in-between-ring domain provides insights for E3-ligase dysfunction in autosomal recessive Parkinson's disease
Beasley, S.A., Hristova, V.A., Shaw, G.S.
Proc. Natl. Acad. Sci. U. S. A. (2007), 104, 3095-3100, PubMed 17360614 , DOI 10.1073/pnas.0610548104 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: O60260 released on 2004-10-11
Title PRKN2_HUMAN Entity E3 ubiquitin-protein ligase parkin

Related entities 1. IBR domain of human Parkin, : 1 : 54 entities Detail

Interaction partners 1. IBR domain of human Parkin, : 37 interactors Detail

More details for 37 interactors identified by 19 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
6	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
7	sodium phosphate	none	25 mM
8	sodium chloride	none	100 mM
9	DTT	none	1 mM
10	DSS	none	0.033 mM

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

4 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

6 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

7 3D HC(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

8 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
6	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
7	sodium phosphate	none	25 mM
8	sodium chloride	none	100 mM
9	DTT	none	1 mM
10	DSS	none	0.033 mM

10 3D HBCBCHCDHD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
6	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
7	sodium phosphate	none	25 mM
8	sodium chloride	none	100 mM
9	DTT	none	1 mM
10	DSS	none	0.033 mM

11 2D NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
6	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
7	sodium phosphate	none	25 mM
8	sodium chloride	none	100 mM
9	DTT	none	1 mM
10	DSS	none	0.033 mM

12 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
1	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
2	sodium phosphate	none	25 mM
3	sodium chloride	none	100 mM
4	DTT	none	1 mM
5	DSS	none	0.033 mM

13 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.95

#	Name	Isotope labeling	Concentration
6	IBR	[U-100% 13C; U-100% 15N]	0.2 mM
7	sodium phosphate	none	25 mM
8	sodium chloride	none	100 mM
9	DTT	none	1 mM
10	DSS	none	0.033 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15074_2jmo.nef
Input source #2: Coordindates	2jmo.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)
2:1:ZN:ZN	1:28:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:33:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:48:CYS:SG	unknown	unknown	n/a
2:1:ZN:ZN	1:56:CYS:SG	unknown	unknown	n/a
2:2:ZN:ZN	1:61:CYS:SG	unknown	unknown	n/a
2:2:ZN:ZN	1:64:CYS:SG	unknown	unknown	n/a
2:2:ZN:ZN	1:69:HIS:NE2	unknown	unknown	n/a
2:2:ZN:ZN	1:73:CYS:SG	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80
GHMGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEAS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEAS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	80	0	0	100.0

Content subtype: combined_15074_2jmo.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_chem_shift_list_1	Warning	794		100.0 (chain: A, length: 80)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	994 (1)	noe	88.7 (chain: A, length: 80)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 423
  - ¹³C chemical shifts: 290
  - ¹⁵N chemical shifts: 81
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	450	423	94.0
¹³C chemical shifts	327	289	88.4
¹⁵N chemical shifts	87	81	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	170	166	97.6
¹³C chemical shifts	160	147	91.9
¹⁵N chemical shifts	76	74	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	280	257	91.8
¹³C chemical shifts	167	142	85.0
¹⁵N chemical shifts	11	7	63.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	26	96.3
¹³C chemical shifts	27	25	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	30	85.7
¹³C chemical shifts	35	16	45.7

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 88.7%
- Total number of restraints: 988
- Weight of restraints: 1.0 (988)
- Potential type of restraints: upper-bound-parabolic (988)
- Range of distance target values: 2.35, 5.5 (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

Keywords E3 ligase, IBR, Parkin, RBR, zinc binding domain

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Found 1 Document (1.171 seconds)

BMRB: 15074

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. IBR domain of human Parkin, : 1 : 54 entities Detail

Interaction partners 1. IBR domain of human Parkin, : 37 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 3 contents Detail