BMRBj - BMREntryMaster

Found 1 Document (0.741 seconds)

BMRB: 17884

2LI9

METAL BINDING DOMAIN OF RAT BETA-AMYLOID

Authors

Polshakov, V., Istrate, A., Kozin, S., Makarov, A.

Assembly

RAT BETA-AMYLOID

Entity

1. rat beta amyloid (polymer, Thiol state: not present), 18 monomers, 1882.964 × 2 Da Detail

XDAEFGHDSG FEVRHQKX

2. ZN (non-polymer), 65.409 Da

Total weight

3831.337 Da

Max. entity weight

1882.964 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

simulated annealing, QM/MM geometry optimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.9 %, Completeness: 76.4 %, Completeness (bb): 63.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	76.4 % (126 of 165)	96.8 % (92 of 95)	48.6 % (34 of 70)
Backbone	63.7 % (51 of 80)	100.0 % (34 of 34)	37.0 % (17 of 46)
Sidechain	82.8 % (82 of 99)	95.1 % (58 of 61)	63.2 % (24 of 38)
Aromatic	78.6 % (22 of 28)	85.7 % (12 of 14)	71.4 % (10 of 14)
Methyl	100.0 % (6 of 6)	100.0 % (3 of 3)	100.0 % (3 of 3)

1. rat beta amyloid

XDAEFGHDSG FEVRHQKX

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
1	rat_beta_amyloid	natural abundance	5 mM
2	Zinc cloride	natural abundance	8 mM
3	TRIS	[U-100% 2H]	20 mM
4	sodium azide	natural abundance	0.1 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
7	rat_beta_amyloid	natural abundance	5 mM
8	Zinc cloride	natural abundance	8 mM
9	TRIS	[U-100% 2H]	20 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LI9, Strand ID: A, B Detail

Release date

2011-10-23

Citation 1

NMR solution structure of rat aβ(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease
Istrate, A.N., Tsvetkov, P.O., Mantsyzov, A.B., Kulikova, A.A., Kozin, S.A., Makarov, A.A., Polshakov, V.I.
Biophys. J. (2012), 102, 136-143, PubMed 22225807 , DOI 10.1016/j.bpj.2011.11.4006 , Abstract

Show more 1 citaion

Citation 2

[Optimization of the methods for small peptide solution structure determination by NMR spectroscopy]
Istrate, A.N., Mantsyzov, A.B., Kozin, S.A., Polshakov, V.I.
Mol. Biol (Mosk). (2010), 44, 1075-1085, PubMed 21290829 , DOI: , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1 entries Detail

BMRB: 19602 released on 2014-11-09
Title Zinc induced dimer of the metal binding domain 1-16 of human amyloid beta-peptide with Alzheimer`s disease pathogenic English mutation H6R

Related entities 1. rat beta amyloid, : 1 : 5 : 73 entities Detail

Interaction partners 1. rat beta amyloid, : 9 interactors Detail

More details for 9 interactors identified by 8 citations

Experiments performed 7 experiments Detail

1 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
7	rat_beta_amyloid	natural abundance	5 mM
8	Zinc cloride	natural abundance	8 mM
9	TRIS	[U-100% 2H]	20 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	natural abundance	100 %

2 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
1	rat_beta_amyloid	natural abundance	5 mM
2	Zinc cloride	natural abundance	8 mM
3	TRIS	[U-100% 2H]	20 mM
4	sodium azide	natural abundance	0.1 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
7	rat_beta_amyloid	natural abundance	5 mM
8	Zinc cloride	natural abundance	8 mM
9	TRIS	[U-100% 2H]	20 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	natural abundance	100 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
1	rat_beta_amyloid	natural abundance	5 mM
2	Zinc cloride	natural abundance	8 mM
3	TRIS	[U-100% 2H]	20 mM
4	sodium azide	natural abundance	0.1 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
7	rat_beta_amyloid	natural abundance	5 mM
8	Zinc cloride	natural abundance	8 mM
9	TRIS	[U-100% 2H]	20 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	natural abundance	100 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
7	rat_beta_amyloid	natural abundance	5 mM
8	Zinc cloride	natural abundance	8 mM
9	TRIS	[U-100% 2H]	20 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	natural abundance	100 %

7 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.1

#	Name	Isotope labeling	Concentration
1	rat_beta_amyloid	natural abundance	5 mM
2	Zinc cloride	natural abundance	8 mM
3	TRIS	[U-100% 2H]	20 mM
4	sodium azide	natural abundance	0.1 %
5	H2O	natural abundance	90 %
6	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_17884_2li9.nef
Input source #2: Coordindates	2li9.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)
1:1:ACE:C	1:2:ASP:N	unknown	unknown	n/a
1:17:LYS:C	1:18:NH2:N	unknown	unknown	n/a
2:1:ACE:C	2:2:ASP:N	unknown	unknown	n/a
2:17:LYS:C	2:18:NH2:N	unknown	unknown	n/a
1:15:HIS:NE2	3:1:ZN:ZN	unknown	unknown	n/a
2:15:HIS:NE2	3:1:ZN:ZN	unknown	unknown	n/a
1:7:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
2:7:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	ACE	ACETYL GROUP	Coordinates
A	17	NH2	AMINO GROUP	Coordinates
B	0	ACE	ACETYL GROUP	Assigned chemical shifts, Coordinates
B	17	NH2	AMINO GROUP	Assigned chemical shifts, Coordinates
C	1	ZN	ZINC ION	Distance restraints, Torsion angle restraints

Sequence alignments

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

0--------10-------
XDAEFGHDSGFEVRHQKX
||||||||||||||||||
XDAEFGHDSGFEVRHQKX
--------10--------

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

0--------10-------
XDAEFGHDSGFEVRHQKX
||||||||||||||||||
XDAEFGHDSGFEVRHQKX
--------10--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0
B	B	18	0	0	100.0

Content subtype: combined_17884_2li9.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	136		100.0 (chain: B, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	542 (1)	noe	88.9 (chain: A, length: 18), 88.9 (chain: B, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	undefined	11.1 (chain: A, length: 18), 11.1 (chain: B, length: 18), 100.0 (chain: C, length: 1)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	21 (21)	.	22.2 (chain: A, length: 18), 22.2 (chain: B, length: 18), 100.0 (chain: C, length: 1)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 101
  - ¹³C chemical shifts: 35
- Completeness of assignments
  - Entity_assemble_ID: B
- 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: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	ARG	HH11	6.813
13	ARG	HH12	6.813
13	ARG	HH21	6.813
13	ARG	HH22	6.813

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	95	96.0
¹³C chemical shifts	72	35	48.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	35	100.0
¹³C chemical shifts	32	10	31.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	60	93.8
¹³C chemical shifts	40	25	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	12	85.7
¹³C chemical shifts	14	10	71.4

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 88.9%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 88.9%
- Total number of restraints: 502
- Weight of restraints: 1.0 (502)
- Potential type of restraints: square-well-parabolic (502)
- Range of distance target values: 1.25, 3.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 11.1%
    - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 11.1%
    - Entity_assembly_ID: C, Chain length: 1, Sequence coverage: 100.0%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 2.1, 2.1 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 22.2%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 22.2%
  - Entity_assembly_ID: C, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 21
- Total number of restraints per polymer type: 21
- Weight of restraints: 1.0 (21)
- Potential type of restraints: square-well-parabolic (21)
- Dihedral angle restraints per residue
  - Chain_ID: C
    None

Keywords Alzheimer s disease, Dimer formation, Isothermal titration calorimetry, NMR solution structure, Rat amyloid beta-peptide, Zinc binding

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.741 seconds)

BMRB: 17884

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. rat beta amyloid, : 1 : 5 : 73 entities Detail

Interaction partners 1. rat beta amyloid, : 9 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail