BMRB Entry 15163

Name: Backbone 1H, 13C, and 15N Chemical Shift Assignments for LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1
Published: 2008-06-27

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR15163

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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:

Backbone 1H, 13C, and 15N Chemical Shift Assignments for LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1

Deposition date:

2007-03-07

Original release date:

2008-06-27

Authors:

Liu, J.; Huang, H.; Yang, Y.; Wu, Jihui; Shi, Yunyu

Citation:

Citation: Liu, Jiangxin; Zhang, Jiahai; Yang, Yinshan; Huang, Hongda; Shen, Weiqun; Hu, Qi; Wang, Xingsheng; Wu, Jihui; Shi, Yunyu. "Conformational change upon ligand binding and dynamics of the PDZ domain from leukemia-associated Rho guanine nucleotide exchange factor" Protein Sci. 17, 1003-1014 (2008).
PubMed: 18411422

Assembly members:

Assembly members:
Rho_guanine_nucleotide_exchange_factor_12, polymer, 89 residues, Formula weight is not available
C-terminal_peptide_of_Plexin-B1, polymer, 8 residues, Formula weight is not available

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: pET15b (+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Rho_guanine_nucleotide_exchange_factor_12: GSHMGLVQRCVIIQKDDNGF GLTVSGDNPVFVQSVKEDGA AMRAGVQTGDRIIKVNGTLV THSNHLEVVKLIKSGSYVAL TVQGRPPGS
C-terminal_peptide_of_Plexin-B1: VENKVTDL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	251
15N chemical shifts	83
1H chemical shifts	616

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	LARG PDZ domain	1
2	C-terminal sequence of Plexin B1	2

Entities:

Entity 1, LARG PDZ domain 89 residues - Formula weight is not available

1

GLY

SER

HIS

MET

GLY

LEU

VAL

GLN

ARG

CYS

2

VAL

ILE

GLN

LYS

ASP

ASN

GLY

PHE

3

GLY

LEU

THR

VAL

SER

GLY

ASP

ASN

PRO

VAL

4

PHE

VAL

GLN

SER

VAL

LYS

GLU

ASP

GLY

ALA

5

ALA

MET

ARG

ALA

GLY

VAL

GLN

THR

GLY

ASP

6

ARG

ILE

LYS

VAL

ASN

GLY

THR

LEU

VAL

7

THR

HIS

SER

ASN

HIS

LEU

GLU

VAL

LYS

8

LEU

ILE

LYS

SER

GLY

SER

TYR

VAL

ALA

LEU

9

THR

VAL

GLN

GLY

ARG

PRO

GLY

SER

Entity 2, C-terminal sequence of Plexin B1 8 residues - Formula weight is not available

1

VAL

GLU

ASN

LYS

VAL

THR

ASP

LEU

Samples:

sample_1: LARG PDZ domain, [U-100% 13C; U-100% 15N], 0.8 mM; C-terminal peptide of Plexin-B1 7.6 mM; phosphate buffer 50 mM; EDTA 5 mM; DTT 1 mM; D2O 10%

sample_2: LARG PDZ domain, [U-100% 13C; U-100% 15N], 0.8 mM; C-terminal peptide of Plexin-B1 7.6 mM; D2O, [U-100% 2H], 99.9%; DTT 1 mM; EDTA 5 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
2D, 13C, 15N-filtered, 13C-edited NOESY	sample_2	isotropic	sample_conditions_1
DQF-COSY	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1

Software:

CNS vCns 1.1, Brunger A. T. etall - structure solution

NMRPipe vNmrpipe 2.2, F.Delaglio - processing

Sparky_3 vSparky 3, T.D.Goddard and D.G.Kneller - data analysis

Molmol_2k.2 vMolmol 2k.2, Koradi - processing

Csi_1.0 vCsi 1.0, David S. Wishart - refinement

NMR spectrometers:

Bruker DMX 500 MHz
Bruker DMX 600 MHz

BMRB	15168
PDB	2OMJ 2OS6
DBJ	BAA20836 BAC65549 BAD89994 BAG57923 BAG65168
GB	AAF36817 AAH63117 AAI52901 AAI56559 AAL87100
REF	NP_001013264 NP_001116505 NP_001185594 NP_001288013 NP_056128
SP	Q8R4H2 Q9NZN5
TPG	DAA22316
AlphaFold	Q8R4H2 Q9NZN5