BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 5194

Title: Three-dimensional Structure of the Synaptotagmin 1 C2B-domain: Synaptotagmin 1 as a Phospholipid Binding Machine   PubMed: 11754837

Authors: Fernandez, Imma; Arac, Demet; Ubach, Josep; Gerber, Stefan; Shin, Ok-ho; Gao, Yan; Anderson, Richard; Sudhof, Thomas; Rizo, Josep

Citation: Fernandez, Imma; Arac, Demet; Ubach, Josep; Gerber, Stefan; Shin, Ok-ho; Gao, Yan; Anderson, Richard; Sudhof, Thomas; Rizo, Josep. "Three-dimensional Structure of the Synaptotagmin 1 C2B-domain: Synaptotagmin 1 as a Phospholipid Binding Machine "  Neuron 32, 1057-1069 (2001).

Assembly members:
synaptotagmin, polymer, 152 residues, 40.078 Da.
CA, non-polymer, 40.078 Da.

Natural source:   Common Name: Rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:   Production method: recombinant technology

Entity Sequences (FASTA):
synaptotagmin: QEKLGDICFSLRYVPTAGKL TVVILEAKNLKKMDVGGLSD PYVKIHLMQNGKRLKKKKTT IKKNTLNPYYNESFSFEVPF EQIQKVQVVVTVLDYDKIGK NDAIGKVFVGYNSTGAELRH WSDMLANPRRPIAQWHTLQV EEEVDAMLAVKK

Data sets:
Data typeCount
1H chemical shifts1150
13C chemical shifts715
15N chemical shifts161

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Synaptotagmin I1
2CALCIUM ION, I2
3CALCIUM ION, II2

Entities:

Entity 1, Synaptotagmin I 152 residues - 40.078 Da.

1   GLNGLULYSLEUGLYASPILECYSPHESER
2   LEUARGTYRVALPROTHRALAGLYLYSLEU
3   THRVALVALILELEUGLUALALYSASNLEU
4   LYSLYSMETASPVALGLYGLYLEUSERASP
5   PROTYRVALLYSILEHISLEUMETGLNASN
6   GLYLYSARGLEULYSLYSLYSLYSTHRTHR
7   ILELYSLYSASNTHRLEUASNPROTYRTYR
8   ASNGLUSERPHESERPHEGLUVALPROPHE
9   GLUGLNILEGLNLYSVALGLNVALVALVAL
10   THRVALLEUASPTYRASPLYSILEGLYLYS
11   ASNASPALAILEGLYLYSVALPHEVALGLY
12   TYRASNSERTHRGLYALAGLULEUARGHIS
13   TRPSERASPMETLEUALAASNPROARGARG
14   PROILEALAGLNTRPHISTHRLEUGLNVAL
15   GLUGLUGLUVALASPALAMETLEUALAVAL
16   LYSLYS

Entity 2, CALCIUM ION, I - Ca - 40.078 Da.

1   CA

Samples:

sample_1: synaptotagmin, [U-15N; U-13C], 1.3 mM; NaCl 150 mM; DTT 2 mM; MES 50 mM; CaCl2 20 mM; D2O 5%; H2O 95%

sample_2: synaptotagmin, [U-15N], 1.3 mM; NaCl 150 mM; DTT 2 mM; MES 50 mM; CaCl2 20 mM; D2O 5%; H2O 95%

sample_3: synaptotagmin, [U-15N], 0.4 mM; NaCl 150 mM; DTT 2 mM; MES 50 mM; EDTA 0.5 mM; D2O 5%; H2O 95%

sample_4: synaptotagmin, [U-10% 13C], 1 mM; NaCl 150 mM; DTT 2 mM; MES 50 mM; CaCl2 20 mM; D2O 5%; H2O 95%

sample_cond_1: pH: 6.3; temperature: 303 K; ionic strength: 150 mM; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
3D 15N-separated NOESYnot availablenot availablesample_cond_1
3D-13C 15N-SEPARATED NOESYnot availablenot availablesample_cond_1
HNHAnot availablenot availablesample_cond_1
1H/13C-HSQCnot availablenot availablesample_cond_1

Software:

NMRPipe v1.8 - processing

VNMR v6.1 - collection

NMRVIEW v4.12 - data analysis

CNS v0.9 - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

BMRB 17838
PDB
GB ABA86948 ELW70523 EPY85161 ETE67808 KFO26676
REF XP_005955385 XP_007441326 XP_008933885 XP_009505833 XP_009699931