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
MolProbity Validation Chart

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Title:
Solution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of L-selectin
Deposition date:
2011-07-25
Original release date:
2012-06-11
Authors:
Gifford, Jessica; Ishida, Hiroaki; Vogel, Hans
Citation:

Citation: Gifford, Jessica; Ishida, Hiroaki; Vogel, Hans. "Structural Insights into Calmodulin-regulated L-selectin Ectodomain Shedding."  J. Biol. Chem. 287, 26513-26527 (2012).
PubMed: 22711531

Assembly members:

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:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET30b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Calmodulin: DQLTEEQIAEFKEAFSLFDK DGDGTITTKELGTVMRSLGQ NPTEAELQDMINEVDADGNG TIDFPEFLTMMARKMKDTDS EEEIREAFRVFDKDGNGYIS AAELRHVMTNLGEKLTDEEV DEMIREADIDGDGQVNYEEF VQMMTAK
L-selectin binding domain peptide: AFIIWLARRLKKGKK

Data sets:
Data typeCount
13C chemical shifts438
15N chemical shifts144
1H chemical shifts287

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Calmodulin1
2L-selectin binding domain peptide2
3CALCIUM ION_13
4CALCIUM ION_23
5CALCIUM ION_33
6CALCIUM ION_43

Entities:

Entity 1, Calmodulin 147 residues - 16535.299 Da.

1   ASPGLNLEUTHRGLUGLUGLNILEALAGLU
2   PHELYSGLUALAPHESERLEUPHEASPLYS
3   ASPGLYASPGLYTHRILETHRTHRLYSGLU
4   LEUGLYTHRVALMETARGSERLEUGLYGLN
5   ASNPROTHRGLUALAGLULEUGLNASPMET
6   ILEASNGLUVALASPALAASPGLYASNGLY
7   THRILEASPPHEPROGLUPHELEUTHRMET
8   METALAARGLYSMETLYSASPTHRASPSER
9   GLUGLUGLUILEARGGLUALAPHEARGVAL
10   PHEASPLYSASPGLYASNGLYTYRILESER
11   ALAALAGLULEUARGHISVALMETTHRASN
12   LEUGLYGLULYSLEUTHRASPGLUGLUVAL
13   ASPGLUMETILEARGGLUALAASPILEASP
14   GLYASPGLYGLNVALASNTYRGLUGLUPHE
15   VALGLNMETMETTHRALALYS

Entity 2, L-selectin binding domain peptide 15 residues - 1834.365 Da.

1   ALAPHEILEILETRPLEUALAARGARGLEU
2   LYSLYSGLYLYSLYS

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-1H COSYsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
2D HMBCsample_1isotropicsample_conditions_1
3D LRCHsample_1isotropicsample_conditions_1
F2-filtered 2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_4isotropicsample_conditions_2
2D 1H-15N IPAP HSQCsample_5isotropicsample_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
AlphaFold O02367 O16305 O96081 P02594 P05932 P14151 P30836 Q28768 Q95198 Q95235

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