BMRB Entry 36696

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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/BMR36696
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
The complex of alpha-synuclein in the presence of PD6
Deposition date:
2024-09-24
Original release date:
2025-12-15
Authors:
Blasco, P.; Li, X.
Citation:

Citation: Zhou, H.; Liang, Z.; Wang, C.; Blasco, P.; Ngai, W.; Xiao, Y.; Chong, T.; Liu, H.; Zheng, C.; Chan, M.; Li, X.. "Development of Nanomolar Affinity Miniprotein Inhibitors Targeting alpha-Synuclein Aggregation as Promising Therapeutic Agents for Parkinson’s Disease"  Ccs Chem. ., .-. (2025).

Assembly members:

Assembly members:
Alpha-synuclein, polymer, 140 residues, 14476.108 Da.
PD6, polymer, 41 residues, 4993.941 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Alpha-synuclein: MDVFMKGLSKAKEGVVAAAE KTKQGVAEAAGKTKEGVLYV GSKTKEGVVHGVATVAEKTK EQVTNVGGAVVTGVTAVAQK TVEGAGSIAAATGFVKKDQL GKNEEGAPQEGILEDMPVDP DNEAYEMPSEEGYQDYEPEA
PD6: HVNELSRIKLRVCQPSRSEI HFKVKMTTHLKKLKESYCQR Q

Data sets:
Data typeCount
13C chemical shifts494
15N chemical shifts152
1H chemical shifts1082

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 140 residues - 14476.108 Da.

1   METASPVALPHEMETLYSGLYLEUSERLYS
2   ALALYSGLUGLYVALVALALAALAALAGLU
3   LYSTHRLYSGLNGLYVALALAGLUALAALA
4   GLYLYSTHRLYSGLUGLYVALLEUTYRVAL
5   GLYSERLYSTHRLYSGLUGLYVALVALHIS
6   GLYVALALATHRVALALAGLULYSTHRLYS
7   GLUGLNVALTHRASNVALGLYGLYALAVAL
8   VALTHRGLYVALTHRALAVALALAGLNLYS
9   THRVALGLUGLYALAGLYSERILEALAALA
10   ALATHRGLYPHEVALLYSLYSASPGLNLEU
11   GLYLYSASNGLUGLUGLYALAPROGLNGLU
12   GLYILELEUGLUASPMETPROVALASPPRO
13   ASPASNGLUALATYRGLUMETPROSERGLU
14   GLUGLYTYRGLNASPTYRGLUPROGLUALA

Entity 2, entity_2 41 residues - 4993.941 Da.

1   HISVALASNGLULEUSERARGILELYSLEU
2   ARGVALCYSGLNPROSERARGSERGLUILE
3   HISPHELYSVALLYSMETTHRTHRHISLEU
4   LYSLYSLEULYSGLUSERTYRCYSGLNARG
5   GLN

Samples:

sample_3: alpha-synuclein, [U-100% 13C; U-100% 15N], 0.50 mM; PD6 1.00 mM; PBS mM; H2O 90%; D2O, [U-2H], 10%

sample_4: alpha-synuclein 0.20 mM; PD6, [U-100% 13C; U-100% 15N], 0.40 mM; PBS mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 0.1627 mM; pH: 7.5; pressure: 1 atm; temperature: 283.15 K

sample_conditions_2: ionic strength: 0.1627 mM; pH: 7.5; pressure: 1 atm; temperature: 283.15 K

Experiments:

NameSampleSample stateSample conditions
(1H-1H-15N)-NOESY-HSQCnot availableisotropicsample_conditions_1
(1H-13C-1H)-NOESY-HSQCnot availableisotropicsample_conditions_1
(1H-1H-15N)-NOESY-HSQCnot availableisotropicsample_conditions_2
(1H-13C-1H)-NOESY-HSQCnot availableisotropicsample_conditions_2
3D HNCACBnot availableisotropicsample_conditions_1
3D CBCA(CO)NHnot availableisotropicsample_conditions_1
2D 1H-13C HSQCnot availableisotropicsample_conditions_1
2D 1H-15N HSQCnot availableisotropicsample_conditions_1
3D TOCSY-HSQCnot availableisotropicsample_conditions_2
2D 1H-13C HSQCnot availableisotropicsample_conditions_2
2D 1H-15N HSQCnot availableisotropicsample_conditions_2
3D HNCACBnot availableisotropicsample_conditions_2
3D CBCA(CO)NHnot availableisotropicsample_conditions_2
3D HCCH-TOCSYnot availableisotropicsample_conditions_1

Software:

Poky, Manthey, Tonelli, Clos II, Rahimi, Markley and Lee - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

Poky, Manthey, Tonelli, Clos II, Rahimi, Markley and Lee - refinement

Poky, Manthey, Tonelli, Clos II, Rahimi, Markley and Lee - peak picking

HADDOCK, Bonvin - structure calculation

NMR spectrometers:

  • Bruker AVANCE NEO 600 MHz

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