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BMRB: 18441

2LSR

Solution structure of harmonin N terminal domain in complex with a exon68 encoded peptide of cadherin23

Authors

Pan, L., Wu, L., Zhang, C., Zhang, M.

Assembly

harmonin

Entity

1. harmonin (polymer, Thiol state: not present), 80 monomers, 9551.977 Da Detail

MDRKVAREFR HKVDFLIEND AEKDYLYDVL RMYHQTMDVA VLVGDLKLVI NEPSRLPLFD AIRPLIPLKH QVEYDQLTPR

2. cadherin23 (polymer, Thiol state: not present), 16 monomers, 1904.254 Da Detail

GSLLKEVLED YLRLKK

Total weight

11456.23 Da

Max. entity weight

9551.977 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.9 %, Completeness: 83.4 %, Completeness (bb): 80.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.4 % (1000 of 1199)	90.6 % (571 of 630)	71.2 % (337 of 473)	95.8 % (92 of 96)
Backbone	80.9 % (458 of 566)	91.5 % (173 of 189)	69.2 % (198 of 286)	95.6 % (87 of 91)
Sidechain	87.2 % (634 of 727)	90.2 % (398 of 441)	82.2 % (231 of 281)	100.0 % (5 of 5)
Aromatic	45.1 % (37 of 82)	90.2 % (37 of 41)	0.0 % (0 of 41)
Methyl	99.2 % (127 of 128)	98.4 % (63 of 64)	100.0 % (64 of 64)

1. harmonin

MDRKVAREFR HKVDFLIEND AEKDYLYDVL RMYHQTMDVA VLVGDLKLVI NEPSRLPLFD AIRPLIPLKH QVEYDQLTPR

2. cadherin23

GSLLKEVLED YLRLKK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 100 mM potassium phosphate,1 mM DTT, and 1 mM EDTA at pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	harmonin	[U-99% 13C; U-99% 15N]		0.6 mM
2	cadherin23	[U-99% 13C; U-99% 15N]		0.6 mM
3	potassium phosphate	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	EDTA	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LSR, Strand ID: A, B Detail

Release date

2012-08-12

Citation

Large protein assemblies formed by multivalent interactions between cadherin23 and harmonin suggest a stable anchorage structure at the tip link of stereocilia
Wu, L., Pan, L., Zhang, C., Zhang, M.
J. Biol. Chem. (2012), 287, 33460-33471, PubMed 22879593 , DOI 10.1074/jbc.M112.378505 , Abstract

Related entities 1. harmonin, : 1 : 7 : 3 : 16 entities Detail

Related entities 2. cadherin23, : 1 : 2 entities Detail

Interaction partners 1. harmonin, : 17 : 1 interactors Detail

More details for 18 interactors identified by 11 citations

Interaction partners 2. cadherin23, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 100 mM potassium phosphate,1 mM DTT, and 1 mM EDTA at pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	harmonin	[U-99% 13C; U-99% 15N]		0.6 mM
2	cadherin23	[U-99% 13C; U-99% 15N]		0.6 mM
3	potassium phosphate	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	EDTA	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 100 mM potassium phosphate,1 mM DTT, and 1 mM EDTA at pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	harmonin	[U-99% 13C; U-99% 15N]		0.6 mM
2	cadherin23	[U-99% 13C; U-99% 15N]		0.6 mM
3	potassium phosphate	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	EDTA	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 100 mM potassium phosphate,1 mM DTT, and 1 mM EDTA at pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	harmonin	[U-99% 13C; U-99% 15N]		0.6 mM
2	cadherin23	[U-99% 13C; U-99% 15N]		0.6 mM
3	potassium phosphate	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	EDTA	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 100 mM potassium phosphate,1 mM DTT, and 1 mM EDTA at pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	harmonin	[U-99% 13C; U-99% 15N]		0.6 mM
2	cadherin23	[U-99% 13C; U-99% 15N]		0.6 mM
3	potassium phosphate	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	EDTA	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 100 mM potassium phosphate,1 mM DTT, and 1 mM EDTA at pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	harmonin	[U-99% 13C; U-99% 15N]		0.6 mM
2	cadherin23	[U-99% 13C; U-99% 15N]		0.6 mM
3	potassium phosphate	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	EDTA	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 100 mM potassium phosphate,1 mM DTT, and 1 mM EDTA at pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	harmonin	[U-99% 13C; U-99% 15N]		0.6 mM
2	cadherin23	[U-99% 13C; U-99% 15N]		0.6 mM
3	potassium phosphate	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	EDTA	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	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_18441_2lsr.nef
Input source #2: Coordindates	2lsr.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

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

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

--100-----110---
GSLLKEVLEDYLRLKK
||||||||||||||||
GSLLKEVLEDYLRLKK
--------10------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	80	0	0	100.0
B	B	16	0	0	100.0

Content subtype: combined_18441_2lsr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1000		97.5 (chain: A, length: 80), 93.8 (chain: B, length: 16)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3062 (1)	noe	97.5 (chain: A, length: 80), 93.8 (chain: B, length: 16)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	88 (1)	hbond	65.0 (chain: A, length: 80), 81.2 (chain: B, length: 16)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	138 (138)	.	81.2 (chain: A, length: 80), 81.2 (chain: B, length: 16)

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: 97.5%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 93.8%
- Total number of assignments
  - ¹H chemical shifts: 587
  - ¹³C chemical shifts: 322
  - ¹⁵N chemical shifts: 91
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 97.5%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 93.8%
- Total number of restraints: 3050
- Weight of restraints: 1.0 (3050)
- Potential type of restraints: square-well-parabolic (3050)
- Range of distance target values: 2.25, 6.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 65.0%
    - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 81.2%
  - Total number of restraints: 88
  - Weight of restraints: 1.0 (88)
  - Potential type of restraints: square-well-parabolic (88)
  - Range of distance target values: 2.0, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 81.2%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 81.2%
- Total number of restraints: 138
- Total number of restraints per polymer type: 138
- Weight of restraints: 1.0 (138)
- Potential type of restraints: square-well-parabolic (138)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords protein complex, usher syndrome