BMRB Entry 15636

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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/BMR15636
MolProbity Validation Chart

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Title:
Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
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 GDYDSMKEPAFREENANFNK

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   GLYASPTYRASPSERMETLYSGLUPROALA
4   PHEARGGLUGLUASNALAASNPHEASNLYS

Samples:

sample_1: CXCL12/SDF1-alpha, [U-100% 13C; U-100% 15N], .31 mM; CXCR4 .775 mM; MES(d13) 25 mM; H2O 90%; D2O 10%

sample_2: CXCR4, [U-100% 13C; U-100% 15N], 1.0 mM; CXCL12/SDF1-alpha 0.625 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 15635 15637 16142 16143 15635
PDB
DBJ BAA28601 BAA28602 BAF85317 BAG11056 BAG34757 BAA01722 BAG35177
EMBL CAG29279 CAA50641 CAA75034
GB AAA97434 AAB39332 AAB39333 AAB40516 AAH39893 AAA03209 AAA16594 AAA16617 AAB81970 AAB93982
REF NP_000600 NP_001009847 NP_001028106 NP_001029058 NP_001171605 NP_001009047 NP_003458 XP_003822867
SP O62657 P48061 P61072 P61073
AlphaFold O62657 P48061 P61072 P61073

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