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 10236

Title: Structure of the C-terminal PID Domain of Fe65L1 Complexed with the Cytoplasmic Tail of APP Reveals a Novel Peptide Binding Mode   PubMed: 18650440

Authors: Li, H.; Koshiba, S.; Tochio, N.; Watanabe, S.; Harada, T.; Inoue, M.; Kigawa, T.; Yokoyama, S.

Citation: Li, H.; Koshiba, S.; Hayashi, F.; Tochio, N.; Tomozawa, T.; Kasai, T.; Yabuki, T.; Motoda, Y.; Harada, T.; Watanabe, S.; Inoue, M.; Hayashizaki, Y.; Tanaka, A.; Kigawa, T.; Yokoyama, S.. "Structure of the C-terminal PID Domain of Fe65L1 Complexed with the Cytoplasmic Tail of APP Reveals a Novel Peptide Binding Mode"  J. Biol. Chem. 283, 27165-27178 (2008).

Assembly members:
peptide from Amyloid beta A4 protein, polymer, 32 residues, Formula weight is not available
C-terminal PID Domain, polymer, 136 residues, Formula weight is not available

Natural source:   Common Name: mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
peptide from Amyloid beta A4 protein: DAAVTPEERHLSKMQQNGYE NPTYKFFEQMQN
C-terminal PID Domain: GSSGSSGPTPKTELVQKFRV QYLGMLPVDRPVGMDTLNSA IENLMTSSSKEDWPSVNMNV ADATVTVISEKNEEEVLVEC RVRFLSFMGVGKDVHTFAFI MDTGNQRFECHVFWCEPNAA NVSEAVQAACSGPSSG

Data sets:
Data typeCount
13C chemical shifts552
15N chemical shifts136
1H chemical shifts1087

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1peptide from Amyloid beta A4 protein1
2C-terminal PID Domain2

Entities:

Entity 1, peptide from Amyloid beta A4 protein 32 residues - Formula weight is not available

1   ASPALAALAVALTHRPROGLUGLUARGHIS
2   LEUSERLYSMETGLNGLNASNGLYTYRGLU
3   ASNPROTHRTYRLYSPHEPHEGLUGLNMET
4   GLNASN

Entity 2, C-terminal PID Domain 136 residues - Formula weight is not available

1   GLYSERSERGLYSERSERGLYPROTHRPRO
2   LYSTHRGLULEUVALGLNLYSPHEARGVAL
3   GLNTYRLEUGLYMETLEUPROVALASPARG
4   PROVALGLYMETASPTHRLEUASNSERALA
5   ILEGLUASNLEUMETTHRSERSERSERLYS
6   GLUASPTRPPROSERVALASNMETASNVAL
7   ALAASPALATHRVALTHRVALILESERGLU
8   LYSASNGLUGLUGLUVALLEUVALGLUCYS
9   ARGVALARGPHELEUSERPHEMETGLYVAL
10   GLYLYSASPVALHISTHRPHEALAPHEILE
11   METASPTHRGLYASNGLNARGPHEGLUCYS
12   HISVALPHETRPCYSGLUPROASNALAALA
13   ASNVALSERGLUALAVALGLNALAALACYS
14   SERGLYPROSERSERGLY

Samples:

sample_1: Fe65L1 PID2, [U-13C; U-15N], 0.37 mM; APP-derived 32-mer peptide 0.37 mM; d-Tris-HCl 20 mM; NaCl 100 mM; d-DTT 1 mM; NaN3 0.02%; H2O 90%; D2O 10%

condition_1: ionic strength: 0.120 M; pH: 7.0; pressure: 1 atm; temperature: 296 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropiccondition_1
3D 1H-13C NOESYsample_1isotropiccondition_1
3D 13C,15N F1-FILTERED 13C F3-EDITED NOESYsample_1isotropiccondition_1
3D 13C,15N F1-FILTERED 15N F3-EDITED NOESYsample_1isotropiccondition_1
2D F2 13C,15N- FILTERED NOESYsample_1isotropiccondition_1

Software:

xwinnmr v3.5, Bruker - collection

NMRPipe v20031121, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.0.4, Johnson, One Moon Scientific - data analysis

Kujira v0.9820, Kobayashi, N. - data analysis

CYANA v1.0.8, Herrmann, Guntert and Wuthrich - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 900 MHz

Related Database Links:

BMRB 10237 10238 10239 15775 10235 10237 10238 10239
PDB
DBJ BAA22264 BAA24230 BAA84580 BAC34997 BAC36369 BAB23568 BAE31851 BAE39700 BAE41482 BAE42990
EMBL CAA30050 CAA30488 CAA31830 CAA66230 CAA68374
GB AAA36829 AAA37139 AAA51722 AAA51726 AAB41502 AAD55360 AAH76587 EDL37768 EDL90042 EGW02447
PRF 1303338A 1403400A 1507304A 1507304B 1507304C
REF NP_000475 NP_001006601 NP_001013036 NP_001070264 NP_001127014 NP_001188342 NP_001188343 NP_001188344 NP_001188345 NP_033816
SP O73683 P05067 P08592 P12023 P53601 Q9DBR4
TPG DAA33655