BMRB Entry 25762

Name: Structure of Pleiotrophin
Published: 2016-03-29

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PDB ID: 2n6f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25762
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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 Pleiotrophin

Deposition date:

2015-08-20

Original release date:

2016-03-29

Authors:

Ryan, Eathen; Shen, Di; Wang, Xu

Citation:

Citation: Ryan, Eathen; Shen, Di; Wang, Xu. "Structural Studies Reveal an Important Role for the Pleiotrophin C Terminus in Mediating Interactions with Chondroitin Sulfate." FEBS J. 283, 1488-1503 (2016).
PubMed: 26896299

Assembly members:

Assembly members:
PTN, polymer, 136 residues, 15347.028 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-15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PTN: GKKEKPEKKVKKSDCGEWQW SVCVPTSGDCGLGTREGTRT GAECKQTMKTQRCKIPCNWK KQFGAECKYQFQAWGECDLN TALKTRTGSLKRALHNAECQ KTVTISKPCGKLTKPKPQAE SKKKKKEGKKQEKMLD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	533
15N chemical shifts	127
1H chemical shifts	620

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Pleiotrophin	1

Entities:

Entity 1, Pleiotrophin 136 residues - 15347.028 Da.

1

GLY

LYS

GLU

LYS

PRO

GLU

LYS

VAL

2

LYS

SER

ASP

CYS

GLY

GLU

TRP

GLN

TRP

3

SER

VAL

CYS

VAL

PRO

THR

SER

GLY

ASP

CYS

4

GLY

LEU

GLY

THR

ARG

GLU

GLY

THR

ARG

THR

5

GLY

ALA

GLU

CYS

LYS

GLN

THR

MET

LYS

THR

6

GLN

ARG

CYS

LYS

ILE

PRO

CYS

ASN

TRP

LYS

7

LYS

GLN

PHE

GLY

ALA

GLU

CYS

LYS

TYR

GLN

8

PHE

GLN

ALA

TRP

GLY

GLU

CYS

ASP

LEU

ASN

9

THR

ALA

LEU

LYS

THR

ARG

THR

GLY

SER

LEU

10

LYS

ARG

ALA

LEU

HIS

ASN

ALA

GLU

CYS

GLN

11

LYS

THR

VAL

THR

ILE

SER

LYS

PRO

CYS

GLY

12

LYS

LEU

THR

LYS

PRO

LYS

PRO

GLN

ALA

GLU

13

SER

LYS

GLU

GLY

LYS

14

GLN

GLU

LYS

MET

LEU

ASP

Samples:

sample_1: PTN, [U-100% 13C; U-100% 15N], 0.6 ± 0.05 mM; D2O 10%; MES 10 mM; sodium chloride 150 mM; H2O 90%

sample_conditions_1: ionic strength: 0.15 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

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

NMRView, Johnson, One Moon Scientific - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Varian INOVA 800 MHz

UNP	P21246
AlphaFold	Q9UCC6