BMRB Entry 11082

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PDB ID: 2rqu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR11082
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of the complex between the DDEF1 SH3 domain and the APC SAMP1 motif

Deposition date:

2009-12-14

Original release date:

2011-05-19

Authors:

Kaieda, Shuji; Matsui, Chiyuki; Mimori-Kiyosue, Yuko; Ikegami, Takahisa

Citation:

Citation: Kaieda, Shuji; Matsui, Chiyuki; Mimori-Kiyosue, Yuko; Ikegami, Takahisa. "Structural basis of the recognition of the SAMP motif of adenomatous polyposis coli by the Src-homology 3 domain." Biochemistry 49, 5143-5153 (2010).
PubMed: 20509626

Assembly members:

Assembly members:
DDEF1 SH3, polymer, 61 residues, 7066.874 Da.
APC SAMP1, polymer, 19 residues, 2050.522 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET32a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DDEF1 SH3: VRRVKTIYDCQADNDDELTF IEGEVIIVTGEEDQEWWIGH IEGQPERKGVFPVSFVHILS D
APC SAMP1: CIISAMPTKSSRKAKKPAQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	341
15N chemical shifts	83
1H chemical shifts	545

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DDEF1 SH3	1
2	APC SAMP1	2

Entities:

Entity 1, DDEF1 SH3 61 residues - 7066.874 Da.

1

VAL

ARG

VAL

LYS

THR

ILE

TYR

ASP

CYS

2

GLN

ALA

ASP

ASN

ASP

GLU

LEU

THR

PHE

3

ILE

GLU

GLY

GLU

VAL

ILE

VAL

THR

GLY

4

GLU

ASP

GLN

GLU

TRP

ILE

GLY

HIS

5

ILE

GLU

GLY

GLN

PRO

GLU

ARG

LYS

GLY

VAL

6

PHE

PRO

VAL

SER

PHE

VAL

HIS

ILE

LEU

SER

7

ASP

Entity 2, APC SAMP1 19 residues - 2050.522 Da.

1

CYS

ILE

SER

ALA

MET

PRO

THR

LYS

SER

2

SER

ARG

LYS

ALA

LYS

PRO

ALA

GLN

Samples:

sample_1: DDEF1 SH3, [U-15N], 0.5 mM; APC SAMP1, [U-15N], 0.5 mM; sodium phosphate 5 mM; DTT, [U-2H], 5 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_2: DDEF1 SH3, [U-13C; U-15N], 0.5 mM; APC SAMP1, [U-13C; U-15N], 0.5 mM; sodium phosphate 5 mM; DTT, [U-2H], 5 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_3: DDEF1 SH3, [U-13C; U-15N], 0.5 mM; APC SAMP1, [U-13C; U-15N], 0.5 mM; sodium phosphate 5 mM; DTT, [U-2H], 5 mM; sodium phosphate 0.02%; D2O 100%

sample_4: DDEF1 SH3, [U-15% 13C; U-15N], 0.5 mM; APC SAMP1, [U-15% 13C; U-15N], 0.5 mM; sodium phosphate 5 mM; DTT, [U-2H], 5 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.2; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D MQ-HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 15N-edited NOESY	sample_1	isotropic	sample_conditions_1
3D aliphatic 13C-edited NOESY	sample_3	isotropic	sample_conditions_1
3D aromatic 13C-edited NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC	sample_4	isotropic	sample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - collection

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

SPARKY v3.115, Goddard and Kneller - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

ARIA v2.2, Rieping, Habeck, Bardiaux, Bernard, Malliavin, and Nilges - refinement

NMR spectrometers:

Bruker DRX 600 MHz
Bruker DRX 800 MHz

BMRB	11081 11153
PDB	2ED1 2RQT 2RQU 2RQU
DBJ	BAA86563 BAC65759 BAE27250 BAE34783 BAE06083 BAG10525
EMBL	CAD97831
GB	AAB82338 AAC98349 AAC98350 AAH02201 AAH48818 AAA03586 AAI11463 AAI11592 AAI11931 AAI13359
REF	NP_001037710 NP_001234925 NP_001263390 NP_001263391 NP_001263392 NP_000029 NP_001069454 NP_001120982 NP_001120983 NP_001193359
SP	Q1AAU6 Q9QWY8 Q9ULH1 P25054
TPG	DAA25893
AlphaFold	Q1AAU6 Q9QWY8 Q9ULH1 P25054