BMRB Entry 34578

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34578
MolProbity Validation Chart

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Title:
Dynamic complex between all-D-enantiomeric peptide D3 with L723P mutant of amyloid precursor protein (APP) 672-726 fragment (amyloid beta 1-55)
Deposition date:
2020-12-01
Original release date:
2021-01-25
Authors:
Bocharov, E.; Volynsky, P.; Okhrimenko, I.; Urban, A.
Citation:

Citation: Bocharov, Eduard; Gremer, Lothar; Urban, Anatoly; Okhrimenko, Ivan; Volynsky, Pavel; Nadezhdin, Kirill; Bocharova, Olga; Kornilov, Daniil; Zagryadskaya, Yuliya; Kamynina, Anna; Kuzmichev, Pavel; Kutzsche, Janine; Bolakhrif, Najoua; Muller-Schiffmann, Andreas; Dencher, Norbert; Arseniev, Alexander; Efremov, Roman; Gordeliy, Valentin; Willbold, Dieter. "All - d - Enantiomeric Peptide D3 Designed for Alzheimer's Disease Treatment Dynamically Interacts with Membrane-Bound Amyloid-beta Precursors"  J. Med. Chem. 64, 16464-16479 (2021).
PubMed: 34739758

Assembly members:

Assembly members:
entity_1, polymer, 55 residues, 5975.009 Da.
entity_2, polymer, 12 residues, 1606.861 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pGEMEX1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV IATVIVITLVMPKKK
entity_2: XXXXXXXXXXXX

Data sets:
Data typeCount
13C chemical shifts217
15N chemical shifts54
1H chemical shifts362

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 55 residues - 5975.009 Da.

1   ASPALAGLUPHEARGHISASPSERGLYTYR
2   GLUVALHISHISGLNLYSLEUVALPHEPHE
3   ALAGLUASPVALGLYSERASNLYSGLYALA
4   ILEILEGLYLEUMETVALGLYGLYVALVAL
5   ILEALATHRVALILEVALILETHRLEUVAL
6   METPROLYSLYSLYS

Entity 2, unit_2 12 residues - 1606.861 Da.

1   DARDPRDAR2TLDARDLEDHI2TLDHIDAR
2   DSGDAR

Samples:

sample_1: APP_L723P_672-726, [U-13C; U-15N], 0.2 mM

sample_2: APP_L723P_672-726, [U-13C; U-15N], 0.2 mM; D3cys(MTSL) 0.2 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.9; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
H/15N-HSQCsample_1isotropicsample_conditions_1
1H/15N-TROSYsample_1isotropicsample_conditions_1
1H/13C/15N-HNCAsample_1isotropicsample_conditions_1
1H/13C/15N-HN(CO)CAsample_1isotropicsample_conditions_1
1H/13C/15N-HNCOsample_1isotropicsample_conditions_1
13C-edited NOESY-HSQCsample_1isotropicsample_conditions_1
1H/13C-HCCH-TOCSYsample_1isotropicsample_conditions_1
15N-edited NOESY-HSQCsample_1isotropicsample_conditions_1
H/15N-HSQCsample_2isotropicsample_conditions_1
1H/15N-TROSYsample_2isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

qMDD, Kazimierczuk & Orekhov - processing

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

GROMACS, Abraham et al - refinement, structure calculation

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks