BMRB Entry 15635

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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/BMR15635
MolProbity Validation Chart

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Title:
Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21
Deposition date:
2008-01-24
Original release date:
2008-11-06
Authors:
Volkman, B.; Veldkamp, C.; Peterson, F.
Citation:

Citation: Veldkamp, Christopher; Seibert, Christoph; Peterson, Francis; De la Cruz, Noberto; Haugner, John; Basnet, Harihar; Sakmar, Thomas; Volkman, Brian. "Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12"  Sci. Signal. 1, ra4-ra4 (2008).
PubMed: 18799424

Assembly members:

Assembly members:
CXCL12/SDF1-alpha, polymer, 70 residues, 8188.810 Da.
CXCR4, polymer, 40 residues, 4518.798 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: pQE30-6HT

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CXCL12/SDF1-alpha: GMKPVSLSYRCPCRFFESHV ARANVKHLKILNTPNCACQI VARLKNNNRQVCIDPKLKWI QEYLEKCLNK
CXCR4: GSMEGISIYTSDNYTEEMGS GDXDSMKEPAFREENANFNK

Data sets:
Data typeCount
13C chemical shifts850
15N chemical shifts212
1H chemical shifts1416

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CXCL12/SDF1-alpha_11
2CXCR4_12
3CXCL12/SDF1-alpha_21
4CXCR4_22

Entities:

Entity 1, CXCL12/SDF1-alpha_1 70 residues - 8188.810 Da.

1   GLYMETLYSPROVALSERLEUSERTYRARG
2   CYSPROCYSARGPHEPHEGLUSERHISVAL
3   ALAARGALAASNVALLYSHISLEULYSILE
4   LEUASNTHRPROASNCYSALACYSGLNILE
5   VALALAARGLEULYSASNASNASNARGGLN
6   VALCYSILEASPPROLYSLEULYSTRPILE
7   GLNGLUTYRLEUGLULYSCYSLEUASNLYS

Entity 2, CXCR4_1 40 residues - 4518.798 Da.

1   GLYSERMETGLUGLYILESERILETYRTHR
2   SERASPASNTYRTHRGLUGLUMETGLYSER
3   GLYASPTYSASPSERMETLYSGLUPROALA
4   PHEARGGLUGLUASNALAASNPHEASNLYS

Samples:

sample_1: CXCL12/SDF1-alpha, [U-100% 13C; U-100% 15N], 0.338 mM; CXCR4 0.970 mM; MES(d13) 25 mM; H2O 90%; D2O 10%

sample_2: CXCR4, [U-100% 13C; U-100% 15N], 1.07 mM; CXCL12/SDF1-alpha 0.67 mM; MES(d13) 25 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 21 mM; pH: 6.8; pressure: 1 atm; temperature: 308 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
3D_13C-F1-filtered_13C-F3-separateded_NOESYsample_1isotropicsample_conditions_1
3D_15N-separated_NOESYsample_2isotropicsample_conditions_1
3D_13C-separated_NOESYsample_2isotropicsample_conditions_1
3D_13C-separated_NOESY (AROMATIC)sample_2isotropicsample_conditions_1
3D_13C-F1-filtered_13C-F3-separateded_NOESYsample_2isotropicsample_conditions_1

Software:

X-PLOR NIH v2.9.3, SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. - refinement

xwinnmr v3.5, Bruker - collection

NMRPipe v2004, Delagio,F. et al. - processing

XEASY v1.3, Eccles, C., Guntert, P., Billeter, M., Wuthrich, K. - data analysis

SPSCAN v1.1.0, R.W. Glaser - data analysis

GARANT v2.1, C. Bartels - data analysis

CYANA v2.1, Guntert, P. - structural calculation

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

BMRB 15633 15636 15637 16142 16143 15636
PDB
DBJ BAA28601 BAA28602 BAF85317 BAG11056 BAG34757
EMBL CAG29279
GB AAA97434 AAB39332 AAB39333 AAB40516 AAH39893
REF NP_000600 NP_001009847 NP_001028106 NP_001029058 NP_001171605
SP O62657 P48061
AlphaFold O62657 P48061

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