BMRB Entry 15637
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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/BMR15637
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Title: Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21 PubMed: 18799424
Deposition date: 2008-01-24 Original release date: 2008-11-06
Authors: Volkman, B.; Veldkamp, C.; Peterson, F.
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).
Assembly members:
CXCL12/SDF1-alpha, polymer, 70 residues, 8188.810 Da.
CXCR4, polymer, 40 residues, 4518.798 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo Sapiens
Experimental source: Production method: recombinant technology Host organism: Excherichia coli
Entity Sequences (FASTA):
CXCL12/SDF1-alpha: GMKPVSLSYRCPCRFFESHV
ARANVKHLKILNTPNCACQI
VARLKNNNRQVCIDPKLKWI
QEYLEKCLNK
CXCR4: GSMEGISIXTSDNXTEEMGS
GDXDSMKEPAFREENANFNK
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 1418 |
| 15N chemical shifts | 211 |
| 13C chemical shifts | 852 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | CXCL12/SDF1-alpha_1 | 1 |
| 2 | CXCR4_1 | 2 |
| 3 | CXCL12/SDF1-alpha_2 | 1 |
| 4 | CXCR4_2 | 2 |
Entities:
Entity 1, CXCL12/SDF1-alpha_1 70 residues - 8188.810 Da.
| 1 | GLY | MET | LYS | PRO | VAL | SER | LEU | SER | TYR | ARG | |
| 2 | CYS | PRO | CYS | ARG | PHE | PHE | GLU | SER | HIS | VAL | |
| 3 | ALA | ARG | ALA | ASN | VAL | LYS | HIS | LEU | LYS | ILE | |
| 4 | LEU | ASN | THR | PRO | ASN | CYS | ALA | CYS | GLN | ILE | |
| 5 | VAL | ALA | ARG | LEU | LYS | ASN | ASN | ASN | ARG | GLN | |
| 6 | VAL | CYS | ILE | ASP | PRO | LYS | LEU | LYS | TRP | ILE | |
| 7 | GLN | GLU | TYR | LEU | GLU | LYS | CYS | LEU | ASN | LYS |
Entity 2, CXCR4_1 40 residues - 4518.798 Da.
| 1 | GLY | SER | MET | GLU | GLY | ILE | SER | ILE | TYS | THR | |
| 2 | SER | ASP | ASN | TYS | THR | GLU | GLU | MET | GLY | SER | |
| 3 | GLY | ASP | TYS | ASP | SER | MET | LYS | GLU | PRO | ALA | |
| 4 | PHE | ARG | GLU | GLU | ASN | ALA | ASN | PHE | ASN | LYS |
Samples:
sample_1: CXCL12/SDF1-alpha, [U-100% 13C; U-100% 15N], 0.338 mM; CXCR4 0.97 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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D_15N-separated_NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY (AROMATIC) | sample_1 | isotropic | sample_conditions_1 |
| 3D_13C-F1-filtered_13C-F3-separateded_NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D_15N-separated_NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY (AROMATIC) | sample_2 | isotropic | sample_conditions_1 |
| 3D_13C-F1-filtered_13C-F3-separateded_NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
xwinnmr v3.5, Bruker - collection
X-PLOR NIH v2.9.3, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMRPipe v2004, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
XEASY v1.3, Bartels et al. - data analysis
SPSCAN v1.1.0, Glaser - peak picking
GARANT v2.1, Bartels, Guntert, Billeter and Wuthrich - chemical shift assignment
NMR spectrometers:
- Bruker DRX 600 MHz
Related Database Links:
| BMRB | 15633 15635 15636 16142 16143 |
| 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 |
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