BMRB Entry 15528

Name: Solution structure of the protease-resistent domain of Xenopus ePABP2
Published: 2007-10-19

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PDB ID: 2jwn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15528
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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:

Solution structure of the protease-resistent domain of Xenopus ePABP2

Deposition date:

2007-10-16

Original release date:

2007-10-19

Authors:

Song, J.; Markley, J.

Citation:

Citation: Song, Jikui; McGivern, Jered; Nichols, Karl; Markley, John; Sheets, Michael. "Structural basis for RNA recognition by a type II poly(A)-binding protein" Proc. Natl. Acad. Sci. U.S.A. 105, 15317-15322 (2008).
PubMed: 18824697

Assembly members:

Assembly members:
ePABP2-trp, polymer, 124 residues, Formula weight is not available

Natural source:

Natural source: Common Name: African clawed frog Taxonomy ID: 8355 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Xenopus Laevis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PVP 56K

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ePABP2-trp: AIAPCMQTTHSKMTAGAYTE GPPQPLSAEEKKEIDKRSVY VGNVDYGSTAQDLEAHFSSC GSINRITILCDKFSGHPKGY AYIEFAERNSVDAAVAMDET VFRGRTIKVLPKRTNMPGIS STDR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	460
15N chemical shifts	124
1H chemical shifts	715

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	protease-resistent domain, chain 1	1
2	protease-resistent domain, chain 2	1

Entities:

Entity 1, protease-resistent domain, chain 1 124 residues - Formula weight is not available

1

ALA

ILE

ALA

PRO

CYS

MET

GLN

THR

HIS

2

SER

LYS

MET

THR

ALA

GLY

ALA

TYR

THR

GLU

3

GLY

PRO

GLN

PRO

LEU

SER

ALA

GLU

4

LYS

GLU

ILE

ASP

LYS

ARG

SER

VAL

TYR

5

VAL

GLY

ASN

VAL

ASP

TYR

GLY

SER

THR

ALA

6

GLN

ASP

LEU

GLU

ALA

HIS

PHE

SER

CYS

7

GLY

SER

ILE

ASN

ARG

ILE

THR

ILE

LEU

CYS

8

ASP

LYS

PHE

SER

GLY

HIS

PRO

LYS

GLY

TYR

9

ALA

TYR

ILE

GLU

PHE

ALA

GLU

ARG

ASN

SER

10

VAL

ASP

ALA

VAL

ALA

MET

ASP

GLU

THR

11

VAL

PHE

ARG

GLY

ARG

THR

ILE

LYS

VAL

LEU

12

PRO

LYS

ARG

THR

ASN

MET

PRO

GLY

ILE

SER

13

SER

THR

ASP

ARG

Samples:

sample_1: ePABP2-trp, [U-100% 13C; U-100% 15N], 1 mM; NaCl 100 mM; NaAc 10 mM

sample_2: ePABP2-trp, [U-100% 13C; U-100% 15N], 0.5 mM; ePABP2-trp 0.5 mM; NaCl 100 mM; NaAc 10 mM

sample_3: ePABP2-trp, [U-100% 15N], 0.5 mM; PEG 5%; NaCl 100 mM; NaAc 10 mM

sample_conditions_1: ionic strength: 100 mM; pH: 5.0; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 100 mM; pH: 5.0; pressure: 1 atm; temperature: 302 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H,15N-HSQC	sample_1	isotropic	sample_conditions_1
1H,13C-HSQC	sample_1	isotropic	sample_conditions_1
HNCACB	sample_1	isotropic	sample_conditions_1
HCCONH	sample_1	isotropic	sample_conditions_1
CBCACONH	sample_1	isotropic	sample_conditions_1
CCONH	sample_1	isotropic	sample_conditions_1
HCCHTOCSY	sample_1	isotropic	sample_conditions_1
HBACONH	sample_1	isotropic	sample_conditions_1
13C-EDITED 1H,1H-NOESY (aliph)	sample_1	isotropic	sample_conditions_1
15N-EDITED 1H,1H-NOESY	sample_1	isotropic	sample_conditions_1
13C,15N filtered, 13C EDITED 1H,1H-NOESY	sample_2	isotropic	sample_conditions_1
15N IPAP HSQC	sample_3	anisotropic	sample_conditions_2
13C-EDITED 1H,1H-NOESY (arom)	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.17.0, SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. - refinement

xwinnmr v3.5, Bruker - collection

NMRPipe v97.027.12.56, Delagio,F. et al. - processing

SPARKY v3.113, Goddard,T.D. and Kneller,D.G. - data analysis

GARANT v2.1, Bartels,C. et al - data analysis

CYANA v2.1, Guntert,P. et al - structural calculation

NMR spectrometers:

Bruker DMX 750 MHz
Varian INOVA 600 MHz
Varian INOVA 900 MHz

PDB	2JWN
GB	AAI70309 AAI70311 AAR26263
REF	NP_001084418
SP	Q6TY21
AlphaFold	Q6TY21