BMRB Entry 10236

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PDB ID: 2roz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR10236
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2008-08-22

Original release date:

2009-03-19

Authors:

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

Citation:

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).
PubMed: 18650440

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- chemical_shift_1

Data type	Count
13C chemical shifts	552
15N chemical shifts	136
1H chemical shifts	1087

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	peptide from Amyloid beta A4 protein	1
2	C-terminal PID Domain	2

Entities:

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

1

ASP

ALA

VAL

THR

PRO

GLU

ARG

HIS

2

LEU

SER

LYS

MET

GLN

ASN

GLY

TYR

GLU

3

ASN

PRO

THR

TYR

LYS

PHE

GLU

GLN

MET

4

GLN

ASN

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

1

GLY

SER

GLY

SER

GLY

PRO

THR

PRO

2

LYS

THR

GLU

LEU

VAL

GLN

LYS

PHE

ARG

VAL

3

GLN

TYR

LEU

GLY

MET

LEU

PRO

VAL

ASP

ARG

4

PRO

VAL

GLY

MET

ASP

THR

LEU

ASN

SER

ALA

5

ILE

GLU

ASN

LEU

MET

THR

SER

LYS

6

GLU

ASP

TRP

PRO

SER

VAL

ASN

MET

ASN

VAL

7

ALA

ASP

ALA

THR

VAL

THR

VAL

ILE

SER

GLU

8

LYS

ASN

GLU

VAL

LEU

VAL

GLU

CYS

9

ARG

VAL

ARG

PHE

LEU

SER

PHE

MET

GLY

VAL

10

GLY

LYS

ASP

VAL

HIS

THR

PHE

ALA

PHE

ILE

11

MET

ASP

THR

GLY

ASN

GLN

ARG

PHE

GLU

CYS

12

HIS

VAL

PHE

TRP

CYS

GLU

PRO

ASN

ALA

13

ASN

VAL

SER

GLU

ALA

VAL

GLN

ALA

CYS

14

SER

GLY

PRO

SER

GLY

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:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	condition_1
3D 1H-13C NOESY	sample_1	isotropic	condition_1
3D 13C,15N F1-FILTERED 13C F3-EDITED NOESY	sample_1	isotropic	condition_1
3D 13C,15N F1-FILTERED 15N F3-EDITED NOESY	sample_1	isotropic	condition_1
2D F2 13C,15N- FILTERED NOESY	sample_1	isotropic	condition_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

BMRB	10237 10238 10239 15775 10235 10237 10238 10239
PDB	2LP1 2ROZ 2YSZ 2YT0 2YT1 3DXC 1WGU 2ROZ 2YSZ 2YT0 2YT1
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
AlphaFold	O73683 P05067 P08592 P12023 P53601 Q9DBR4