BMRB Entry 17807
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17807
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Title: Solution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of L-selectin PubMed: 22711531
Deposition date: 2011-07-25 Original release date: 2012-06-11
Authors: Gifford, Jessica; Ishida, Hiroaki; Vogel, Hans
Citation: Gifford, Jessica; Ishida, Hiroaki; Vogel, Hans. "Structural Insights into Calmodulin-regulated L-selectin Ectodomain Shedding." J. Biol. Chem. 287, 26513-26527 (2012).
Assembly members:
Calmodulin, polymer, 147 residues, 16535.299 Da.
L-selectin binding domain peptide, polymer, 15 residues, 1834.365 Da.
CA, non-polymer, 40.078 Da.
Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Calmodulin: DQLTEEQIAEFKEAFSLFDK
DGDGTITTKELGTVMRSLGQ
NPTEAELQDMINEVDADGNG
TIDFPEFLTMMARKMKDTDS
EEEIREAFRVFDKDGNGYIS
AAELRHVMTNLGEKLTDEEV
DEMIREADIDGDGQVNYEEF
VQMMTAK
L-selectin binding domain peptide: AFIIWLARRLKKGKK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 438 |
| 15N chemical shifts | 144 |
| 1H chemical shifts | 287 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Calmodulin | 1 |
| 2 | L-selectin binding domain peptide | 2 |
| 3 | CALCIUM ION_1 | 3 |
| 4 | CALCIUM ION_2 | 3 |
| 5 | CALCIUM ION_3 | 3 |
| 6 | CALCIUM ION_4 | 3 |
Entities:
Entity 1, Calmodulin 147 residues - 16535.299 Da.
| 1 | ASP | GLN | LEU | THR | GLU | GLU | GLN | ILE | ALA | GLU | ||||
| 2 | PHE | LYS | GLU | ALA | PHE | SER | LEU | PHE | ASP | LYS | ||||
| 3 | ASP | GLY | ASP | GLY | THR | ILE | THR | THR | LYS | GLU | ||||
| 4 | LEU | GLY | THR | VAL | MET | ARG | SER | LEU | GLY | GLN | ||||
| 5 | ASN | PRO | THR | GLU | ALA | GLU | LEU | GLN | ASP | MET | ||||
| 6 | ILE | ASN | GLU | VAL | ASP | ALA | ASP | GLY | ASN | GLY | ||||
| 7 | THR | ILE | ASP | PHE | PRO | GLU | PHE | LEU | THR | MET | ||||
| 8 | MET | ALA | ARG | LYS | MET | LYS | ASP | THR | ASP | SER | ||||
| 9 | GLU | GLU | GLU | ILE | ARG | GLU | ALA | PHE | ARG | VAL | ||||
| 10 | PHE | ASP | LYS | ASP | GLY | ASN | GLY | TYR | ILE | SER | ||||
| 11 | ALA | ALA | GLU | LEU | ARG | HIS | VAL | MET | THR | ASN | ||||
| 12 | LEU | GLY | GLU | LYS | LEU | THR | ASP | GLU | GLU | VAL | ||||
| 13 | ASP | GLU | MET | ILE | ARG | GLU | ALA | ASP | ILE | ASP | ||||
| 14 | GLY | ASP | GLY | GLN | VAL | ASN | TYR | GLU | GLU | PHE | ||||
| 15 | VAL | GLN | MET | MET | THR | ALA | LYS |
Entity 2, L-selectin binding domain peptide 15 residues - 1834.365 Da.
| 1 | ALA | PHE | ILE | ILE | TRP | LEU | ALA | ARG | ARG | LEU | ||||
| 2 | LYS | LYS | GLY | LYS | LYS |
Entity 3, CALCIUM ION_1 - Ca - 40.078 Da.
| 1 | CA |
Samples:
sample_1: Calmodulin, [U-13C; U-15N], 0.5 – 0.8 mM; L-selectin binding domain peptide0.5 – 0.8 mM; CALCIUM ION 4 mM; DSS 0.5 mM; potassium chloride 100 mM; sodium azide 0.03%; Bis-Tris 20 mM; H2O 90%; D2O 10%
sample_2: Calmodulin, [U-2H; U-15N], 0.5 – 0.8 mM; L-selectin binding domain peptide0.5 – 0.8 mM; CALCIUM ION 4 mM; DSS 0.5 mM; potassium chloride 100 mM; sodium azide 0.03%; Bis-Tris 20 mM; H2O 90%; D2O 10%
sample_3: Calmodulin, [1H/13C-methyl Met; U-2H; U-15N], 0.5 – 0.8 mM; L-selectin binding domain peptide0.5 – 0.8 mM; CALCIUM ION 4 mM; DSS 0.5 mM; potassium chloride 100 mM; sodium azide 0.03%; Bis-Tris 20 mM; D2O 100%
sample_4: Calmodulin, [U-13C; U-15N], 0.5 – 0.8 mM; L-selectin binding domain peptide0.5 – 0.8 mM; CALCIUM ION 4 mM; DSS 0.5 mM; potassium chloride 300 mM; sodium azide 0.03%; Bis-Tris 20 mM; H2O 90%; D2O 10%
sample_5: Calmodulin, [U-13C; U-15N], 0.5 – 0.8 mM; L-selectin binding domain peptide0.5 – 0.8 mM; CALCIUM ION 4 mM; DSS 0.5 mM; potassium chloride 300 mM; sodium azide 0.03%; Bis-Tris 20 mM; Pf1 phage 16 w/v; D2O 10%; H2O 90%
sample_conditions_1: ionic strength: 0.1 M; pH: 6.8; pressure: 1 atm; temperature: 303 K
sample_conditions_2: ionic strength: 0.3 M; pH: 6.8; pressure: 1 atm; temperature: 303 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 2D HMBC | sample_1 | isotropic | sample_conditions_1 |
| 3D LRCH | sample_1 | isotropic | sample_conditions_1 |
| F2-filtered 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N IPAP HSQC | sample_4 | isotropic | sample_conditions_2 |
| 2D 1H-15N IPAP HSQC | sample_5 | isotropic | sample_conditions_2 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking
CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, refinement, structure solution
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution
ProcheckNMR, Laskowski and MacArthur - data analysis
TALOS, Cornilescu, Delaglio and Bax - data analysis
Molmol, Koradi, Billeter and Wuthrich - data analysis
xwinnmr, Bruker Biospin - collection
NMR spectrometers:
- Bruker Avance 500 MHz
Related Database Links:
| BMRB | 15184 15185 15186 15187 15188 15191 15470 15624 15650 15852 1634 16418 16465 1648 16764 17264 17360 17771 18027 18028 18556 19036 19238 19586 19604 25253 25257 26503 26626 26627 4056 4270 4284 4310 |
| PDB | |
| DBJ | BAA08302 BAA11896 BAA19786 BAA19787 BAA19788 BAA01613 BAF46391 BAG35555 BAG60862 BAI47122 |
| EMBL | CAA10601 CAA32050 CAA32062 CAA32119 CAA32120 CAA34203 CAA34275 CAB43536 CAB55488 |
| GB | AAA35635 AAA35641 AAA37365 AAA40862 AAA40863 AAA67896 AAB18246 AAB18247 AAB18248 AAB40903 |
| PIR | JC1305 MCON |
| PRF | 0409298A 0608335A 1516348A |
| REF | NP_001008160 NP_001009759 NP_001027633 NP_001039714 NP_001040234 NP_000646 NP_001009074 NP_001036228 NP_001075821 NP_001082779 |
| SP | O02367 O16305 O96081 P02594 P05932 P14151 P30836 Q28768 Q95198 Q95235 |
| TPG | DAA13808 DAA18029 DAA19590 DAA24777 DAA24988 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts