BMRB Entry 16145

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16145
MolProbity Validation Chart

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Title:
Structure of SDF-1/CXCL12
Deposition date:
2009-01-28
Original release date:
2009-06-25
Authors:
Volkman, B.; Veldkamp, C.; Peterson, F.
Citation:

Citation: Veldkamp, C.; Ziarek, J.; Su, J.; Basnet, H.; Lennertz, R.; Weiner, J.; Peterson, F.; Baker, J.; Volkman, B.. "Monomeric structure of the cardioprotective chemokine SDF-1/CXCL12"  Protein Sci. 18, 1359-1369 (2009).
PubMed: 19551879

Assembly members:

Assembly members:
CXCL12/SDF1-alpha, polymer, 70 residues, 8122.656 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   Vector: pQE30

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CXCL12/SDF1-alpha: GSKPVSLSYRCPCRFFESHV ARANVKHLKILNTPNCALQI VARLKNNNRQVCIDPKLKWI QEYLEKALNK

Data sets:
Data typeCount
13C chemical shifts319
15N chemical shifts76
1H chemical shifts528

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1CXCL12/SDF1-alpha1

Entities:

Entity 1, CXCL12/SDF1-alpha 70 residues - 8122.656 Da.

1   GLYSERLYSPROVALSERLEUSERTYRARG
2   CYSPROCYSARGPHEPHEGLUSERHISVAL
3   ALAARGALAASNVALLYSHISLEULYSILE
4   LEUASNTHRPROASNCYSALALEUGLNILE
5   VALALAARGLEULYSASNASNASNARGGLN
6   VALCYSILEASPPROLYSLEULYSTRPILE
7   GLNGLUTYRLEUGLULYSALALEUASNLYS

Samples:

sample_1: CXCL12/SDF1-alpha, [U-100% 13C; U-100% 15N], 1.2 mM; H2O 90%; D2O 10%; MES 20 mM

sample_conditions_1: ionic strength: 0.001 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D_15N-separated_NOESYsample_1isotropicsample_conditions_1
3D_13C-separated_NOESYsample_1isotropicsample_conditions_1
3D_13C-separated_NOESY (AROMATIC)sample_1isotropicsample_conditions_1

Software:

X-PLOR NIH v2.9.3, Schwieters, Kuszewski, Tjandra and Clore - refinement

TOPSPIN, Bruker Biospin - collection

NMRPipe v2004, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY v1.3, Bartels et al. - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker DRX 600 MHz

Related Database Links:

BMRB 16142 16143 16519
PDB
DBJ BAA28601 BAA28602 BAF85317 BAG11056 BAG34757
EMBL CAE11785 CAG29279
GB AAA97434 AAB39332 AAB39333 AAB40516 AAH39893
REF NP_000600 NP_001009580 NP_001009847 NP_001012495 NP_001028106
SP O62657 P48061
AlphaFold O62657 P48061

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SPARKY: Backbone or all simulated peaks