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Biological Magnetic Resonance Data Bank


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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   PubMed: 18803400

Deposition date: 2007-08-06 Original release date: 2008-10-29

Authors: Lee, Young-Tae; Chazin, Walter

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).

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

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

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

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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts