BMRB: 10236

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

Authors

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

Assembly

peptide from Amyloid beta A4 protein, Amyloid beta A4 precursor protein-binding family B member 2

Entity

1. peptide from Amyloid beta A4 protein (polymer, Thiol state: not present), 32 monomers, 3832.146 Da Detail

DAAVTPEERH LSKMQQNGYE NPTYKFFEQM QN

2. C-terminal PID Domain (polymer, Thiol state: all free), 136 monomers, 14738.43 Da Detail

GSSGSSGPTP KTELVQKFRV QYLGMLPVDR PVGMDTLNSA IENLMTSSSK EDWPSVNMNV ADATVTVISE KNEEEVLVEC RVRFLSFMGV GKDVHTFAFI MDTGNQRFEC HVFWCEPNAA NVSEAVQAAC SGPSSG

Total weight

18570.576 Da

Max. entity weight

14738.43 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 86.0 %, Completeness (bb): 82.8 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	86.0 % (1630 of 1895)	93.7 % (920 of 982)	77.9 % (571 of 733)	77.2 % (139 of 180)
Backbone	82.8 % (820 of 990)	92.0 % (311 of 338)	77.9 % (384 of 493)	78.6 % (125 of 159)
Sidechain	88.1 % (936 of 1062)	94.6 % (609 of 644)	78.8 % (313 of 397)	66.7 % (14 of 21)
Aromatic	80.7 % (121 of 150)	94.7 % (71 of 75)	65.8 % (48 of 73)	100.0 % (2 of 2)
Methyl	92.9 % (143 of 154)	96.1 % (74 of 77)	89.6 % (69 of 77)

1. peptide from Amyloid beta A4 protein

DAAVTPEERH LSKMQQNGYE NPTYKFFEQM QN

2. C-terminal PID Domain

GSSGSSGPTP KTELVQKFRV QYLGMLPVDR PVGMDTLNSA IENLMTSSSK EDWPSVNMNV ADATVTVISE KNEEEVLVEC RVRFLSFMGV GKDVHTFAFI MDTGNQRFEC HVFWCEPNAA NVSEAVQAAC SGPSSG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 296 (±0.1) K, pH 7.0 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	Fe65L1 PID2	[U-13C; U-15N]	protein	0.37 mM
2	APP-derived 32-mer peptide	natural abundance	protein	0.37 mM
3	d-Tris-HCl		buffer	20 mM
4	NaCl		salt	100 mM
5	d-DTT		salt	1 mM
6	NaN3		salt	0.02 %
7	H2O		solvent	90 %
8	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.05 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.05 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.05 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.28 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

Calculated from 20 models in PDB: 2ROZ, Strand ID: A, B Detail

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Release date

2009-03-18

Citation

Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode
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.
J. Biol. Chem. (2008), 283, 27165-27178, PubMed 18650440 , DOI 10.1074/jbc.M803892200 , Abstract

Entries sharing articles BMRB: 4 entries Detail

Related entities 1. peptide from Amyloid beta A4 protein, : 1 : 18 : 2 : 3 : 13 entities Detail

Related entities 2. C-terminal PID Domain, : 1 : 2 : 3 : 40 entities Detail

Interaction partners 1. peptide from Amyloid beta A4 protein, : 90 interactors Detail

Experiments performed 5 experiments Detail