BMRB Entry 15418

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15418
MolProbity Validation Chart

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Title:
NMR structure of the S100A6 dimer in complex with a binding fragment of the Siah-1 interacting protein
Deposition date:
2007-08-06
Original release date:
2008-10-29
Authors:
Lee, Young-Tae; Chazin, Walter
Citation:

Citation: Lee, Young-Tae; Dimitrova, Yoana; Schneider, Gabriela; Ridenour, Whitney; Bhattacharya, Shibani; Soss, Sarah; Caprioli, Richard; Filipek, Anna; Chazin, Walter. "Structure of the S100A6 complex with a fragment from the C-terminal domain of Siah-1 interacting protein: a novel mode for S100 protein target recognition"  Biochemistry 47, 10921-10932 (2008).
PubMed: 18803400

Assembly members:

Assembly members:
S100A6, polymer, 90 residues, 10168.827 Da.
SIP(189-219), polymer, 35 residues, 3648.154 Da.

Natural source:

Natural source:   Common Name: rabbit   Taxonomy ID: 9986   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Oryctolagus cuniculus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET1120

Entity Sequences (FASTA):

Entity Sequences (FASTA):
S100A6: MASPLDQAIGLLIGIFHKYS GKEGDKHTLSKKELKELIQK ELTIGSKLQDAEIVKLMDDL DRNKDQEVNFQEYITFLGAL AMIYNEALKG
SIP(189-219): GPGSSEGLMNVLKKIYEDGD DDMKRTINKAWVESR

Data sets:
Data typeCount
13C chemical shifts295
15N chemical shifts113
1H chemical shifts391

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1protein, 11
2protein, 21
3peptide, 12
4peptide, 22

Entities:

Entity 1, protein, 1 90 residues - 10168.827 Da.

1   METALASERPROLEUASPGLNALAILEGLY
2   LEULEUILEGLYILEPHEHISLYSTYRSER
3   GLYLYSGLUGLYASPLYSHISTHRLEUSER
4   LYSLYSGLULEULYSGLULEUILEGLNLYS
5   GLULEUTHRILEGLYSERLYSLEUGLNASP
6   ALAGLUILEVALLYSLEUMETASPASPLEU
7   ASPARGASNLYSASPGLNGLUVALASNPHE
8   GLNGLUTYRILETHRPHELEUGLYALALEU
9   ALAMETILETYRASNGLUALALEULYSGLY

Entity 2, peptide, 1 35 residues - 3648.154 Da.

First 4 residues (GPGS) represents residual tag.

1   GLYPROGLYSERSERGLUGLYLEUMETASN
2   VALLEULYSLYSILETYRGLUASPGLYASP
3   ASPASPMETLYSARGTHRILEASNLYSALA
4   TRPVALGLUSERARG

Samples:

D-SIP_U-A6: SIP(189-219), [U-100% 13C; U-100% 15N], 1 mM; S100A6 1 mM; TRIS, [U-2H], 0.05 mM; Ca2+ 0.01 mM; H2O 93%; D2O 5%; d-TFE 2%

15-SIP_U-A6: SIP(189-219), [U-100% 15N], 1 mM; S100A6 1 mM; TRIS, [U-2H], 0.05 mM; Ca2+ 0.01 mM; H2O 93%; D2O 5%; d-TFE 2%

13-SIP_U-A6: SIP(189-219), [U-100% 13C], 1 mM; S100A6 1 mM; TRIS, [U-2H], 0.05 mM; Ca2+ 0.01 mM; D2O 98%; d-TFE 2%

13-SIP_15-A6: SIP(189-219), [U-100% 13C], 2.3 mM; S100A6, [U-100% 15N], 2.3 mM; TRIS, [U-2H], 0.05 mM; Ca2+ 0.01 mM; H2O 93%; D2O 5%; d-TFE 2%

U-SIP_D_A6: SIP(189-219) 1 mM; S100A6, [U-100% 13C; U-100% 15N], 1 mM; TRIS, [U-2H], 0.05 mM; Ca2+ 0.01 mM; H2O 93%; D2O 5%; d-TFE 2%

All_samples: ionic strength: 0.08 M; pH: 6.5; pressure: 1 atm; temperature: 318 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15-SIP_U-A6isotropicAll_samples
3D 1H-15N NOESY15-SIP_U-A6isotropicAll_samples
3D HNCAD-SIP_U-A6isotropicAll_samples
3D HNCACBD-SIP_U-A6isotropicAll_samples
3D CBCA(CO)NHD-SIP_U-A6isotropicAll_samples
3D HNCOD-SIP_U-A6isotropicAll_samples
2D 1H-13C HSQC13-SIP_U-A6isotropicAll_samples
3D HCCH-TOCSY13-SIP_U-A6isotropicAll_samples
3D 1H-13C NOESY13-SIP_U-A6isotropicAll_samples
3D 13C-filtered 15N-edited NOESY13-SIP_15-A6isotropicAll_samples
2D 1H-15N HSQCU-SIP_D_A6isotropicAll_samples
3D HNCAU-SIP_D_A6isotropicAll_samples
3D CBCA(CO)NHU-SIP_D_A6isotropicAll_samples

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - Structure calculation

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Koll - refinement

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 4430
PDB
DBJ BAA01707 BAE01932 BAG36086 BAG52713
REF NP_001182671 NP_001004208 NP_001007215 NP_001029981 NP_001127554 NP_001253590
SP P30801 Q3T168 Q4R4P3 Q5R6Z8 Q6AYK6 Q9CXW3
EMBL CAA22910 CAH92462
GB AAC16757 AAC21458 AAG34170 AAH05975 AAH22352
TPG DAA21139
AlphaFold P30801 Q3T168 Q4R4P3 Q5R6Z8 Q6AYK6 Q9CXW3

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