BMRB Entry 17364

Name: The solution structure of the PTB Domain of TENC1 in complex with the peptide of DLC1
Published: 2012-06-04

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PDB ID: 2loz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17364
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

The solution structure of the PTB Domain of TENC1 in complex with the peptide of DLC1

Deposition date:

2010-12-14

Original release date:

2012-06-04

Authors:

Liu, Changdong; Chen, Lihong; Feng, Rui; Zhu, Guang

Citation:

Citation: Chen, Lihong; Liu, Changdong; Ko, Frankie Chi Fat; Xu, Naining; Ng, Irene Oi-Lin; Yam, Judy Wai Ping; Zhu, Guang. "Solution structure of the phosphotyrosine binding (PTB) domain of human tensin2 protein in complex with deleted in liver cancer 1 (DLC1) peptide reveals a novel peptide binding mode." J. Biol. Chem. 287, 26104-26114 (2012).
PubMed: 22645138

Assembly members:

Assembly members:
PTB_domian, polymer, 147 residues, 15983.273 Da.
DLC1_peptide, polymer, 21 residues, 2243.518 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: PET

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PTB_domian: MSTAADLLRQGAACSVLYLT SVETESLTGPQAVARASSAA LSCSPRPTPAVVHFKVSAQG ITLTDNQRKLFFRRHYPVNS ITFSSTDPQDRRWTNPDGTT SKIFGFVAKKPGSPWENVCH LFAELDPDQPAGAIVTFITK VLLGQRK
DLC1_peptide: IPEDHKPGTFPKALTNGSFS P

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	484
15N chemical shifts	133
1H chemical shifts	992

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PTB domian	1
2	DLC1 peptide	2

Entities:

Entity 1, PTB domian 147 residues - 15983.273 Da.

1

MET

SER

THR

ALA

ASP

LEU

ARG

GLN

2

GLY

ALA

CYS

SER

VAL

LEU

TYR

LEU

THR

3

SER

VAL

GLU

THR

GLU

SER

LEU

THR

GLY

PRO

4

GLN

ALA

VAL

ALA

ARG

ALA

SER

ALA

5

LEU

SER

CYS

SER

PRO

ARG

PRO

THR

PRO

ALA

6

VAL

HIS

PHE

LYS

VAL

SER

ALA

GLN

GLY

7

ILE

THR

LEU

THR

ASP

ASN

GLN

ARG

LYS

LEU

8

PHE

ARG

HIS

TYR

PRO

VAL

ASN

SER

9

ILE

THR

PHE

SER

THR

ASP

PRO

GLN

ASP

10

ARG

TRP

THR

ASN

PRO

ASP

GLY

THR

11

SER

LYS

ILE

PHE

GLY

PHE

VAL

ALA

LYS

12

PRO

GLY

SER

PRO

TRP

GLU

ASN

VAL

CYS

HIS

13

LEU

PHE

ALA

GLU

LEU

ASP

PRO

ASP

GLN

PRO

14

ALA

GLY

ALA

ILE

VAL

THR

PHE

ILE

THR

LYS

15

VAL

LEU

GLY

GLN

ARG

LYS

Entity 2, DLC1 peptide 21 residues - 2243.518 Da.

1

ILE

PRO

GLU

ASP

HIS

LYS

PRO

GLY

THR

PHE

2

PRO

LYS

ALA

LEU

THR

ASN

GLY

SER

PHE

SER

3

PRO

Samples:

sample_1: PTB domian, [U-100% 13C; U-100% 15N], 0.6-0.8 mM; potassium phosphate 100 mM; sodium chloride 100 mM; EDTA 1 mM; DLC1 peptide 1.2-1.4 mM; H2O 90 mM; D2O 10 mM

sample_2: PTB domian, [U-100% 13C; U-100% 15N], 0.6-0.8 mM; DLC1 peptide 1.2-1.4 mM; potassium phosphate 100 mM; sodium chloride 100 mM; EDTA 1 mM; D2O 100 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 13C/15N filtered-13C edited NOESY	sample_2	isotropic	sample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

HADDOCK v1.3, Alexandre Bonvin - structure solution

ProcheckNMR, Laskowski and MacArthur - geometry optimization

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 750 MHz
Varian INOVA 800 MHz

BMRB	10318
PDB	2DKQ 2LOZ 3HQC 2LOZ
DBJ	BAA83027 BAG09960 BAG54765 BAB21814 BAF82423 BAF84371 BAG10131 BAG61122
EMBL	CAB70815 CAH56176
GB	AAH54099 AAI10855 AAI29829 AAI29830 AAI31504 AAB81637 AAB87700 AAH54511 AAK97501 ACE86794
REF	NP_056134 NP_736610 NP_938072 XP_001102202 XP_001790253 NP_001157743 NP_006085 NP_872584 XP_001092830 XP_003256738
SP	Q63HR2 Q96QB1
TPG	DAA29990
PIR	G59435
AlphaFold	Q63HR2 Q96QB1