BMRB Entry 18840

Name: The ZZ domain of cytoplasmic polyadenylation element binding protein 1 (CPEB1)
Published: 2013-04-01

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PDB ID: 2m13
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18840
MolProbity Validation Chart

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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:

The ZZ domain of cytoplasmic polyadenylation element binding protein 1 (CPEB1)

Deposition date:

2012-11-14

Original release date:

2013-04-01

Authors:

Lee, Brian; Merkel, Daniel; Wells, Sarah; Hilburn, Bryce; Elazzouzi, Fatima; Perez-Alvarado, Gabriela

Citation:

Citation: Merkel, Daniel; Wells, Sarah; Hilburn, Bryce; Elazzouzi, Fatima; Perez-Alvarado, Gabriela; Lee, Brian. "The C-Terminal Region of Cytoplasmic Polyadenylation Element Binding Protein Is a ZZ Domain with Potential for Protein-Protein Interactions." J. Mol. Biol. 425, 2015-2026 (2013).
PubMed: 23500490

Assembly members:

Assembly members:
CPEB1-ZZ_G-P-504-566, polymer, 65 residues, 7768.881 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CPEB1-ZZ_G-P-504-566: GPVQIDPYLEDSLCHICSSQ PGPFFCRDQVCFKYFCRSCW HWRHSMEGLRHHSPLMRNQK NRDSS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	283
15N chemical shifts	76
1H chemical shifts	430

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CPEB1-ZZ_G-P-504-566	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, CPEB1-ZZ_G-P-504-566 65 residues - 7768.881 Da.

Residues Gly502 and Pro503 are non-native remnants of HRV 3C digest from MBP fusion

1

GLY

PRO

VAL

GLN

ILE

ASP

PRO

TYR

LEU

GLU

2

ASP

SER

LEU

CYS

HIS

ILE

CYS

SER

GLN

3

PRO

GLY

PRO

PHE

CYS

ARG

ASP

GLN

VAL

4

CYS

PHE

LYS

TYR

PHE

CYS

ARG

SER

CYS

TRP

5

HIS

TRP

ARG

HIS

SER

MET

GLU

GLY

LEU

ARG

6

HIS

SER

PRO

LEU

MET

ARG

ASN

GLN

LYS

7

ASN

ARG

ASP

SER

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

ZZ-504: CPEB1-ZZ G-P-504-566, [U-100% 13C; U-100% 15N], 0.3 mM; TRIS 20 mM; sodium chloride 200 mM; DTT 1 mM; H2O 90%; D2O 10%

ZZ-498: CPEB1-ZZ T498S-566, [U-100% 13C; U-100% 15N], 0.3 mM; potassium phosphate 50 mM; potassium chloride 200 mM; DTT 5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 200 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	ZZ-504	isotropic	sample_conditions_1
2D 1H-15N HSQC	ZZ-498	isotropic	sample_conditions_1
2D 1H-1H NOESY	ZZ-504	isotropic	sample_conditions_1
2D 1H-1H NOESY	ZZ-498	isotropic	sample_conditions_1
2D 1H-13C ct-HSQC aliphatic	ZZ-504	isotropic	sample_conditions_1
2D 1H-13C ct-HSQC aliphatic	ZZ-498	isotropic	sample_conditions_1
2D 1H-13C HMQC aromatic	ZZ-504	isotropic	sample_conditions_1
2D 1H-13C HMQC aromatic	ZZ-498	isotropic	sample_conditions_1
2D 1H-15N HMQC 2JNH	ZZ-498	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD	ZZ-504	isotropic	sample_conditions_1
3D HNCO	ZZ-504	isotropic	sample_conditions_1
3D HNCO	ZZ-498	isotropic	sample_conditions_1
3D HNCA	ZZ-504	isotropic	sample_conditions_1
3D HNCA	ZZ-498	isotropic	sample_conditions_1
3D HNCACB	ZZ-504	isotropic	sample_conditions_1
3D CBCA(CO)NH	ZZ-504	isotropic	sample_conditions_1
3D CBCA(CO)NH	ZZ-498	isotropic	sample_conditions_1
3D HCCH-COSY	ZZ-504	isotropic	sample_conditions_1
3D HCCH-COSY	ZZ-498	isotropic	sample_conditions_1
3D 1H-15N/13C NOESY	ZZ-504	isotropic	sample_conditions_1
3D 1H-15N/13C NOESY	ZZ-498	isotropic	sample_conditions_1
3D HCCH-TOCSY	ZZ-504	isotropic	sample_conditions_1
3D C(CO)NH	ZZ-504	isotropic	sample_conditions_1

Software:

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v1.0.5, Guntert, Mumenthaler and Wuthrich - refinement

TALOS_plus, Shen, Delaglio, Cornilescu and Bax - chemical shift calculation

Molmol, Koradi, Billeter and Wuthrich - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMRView v8.0.3, Johnson, One Moon Scientific - data analysis

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

NMR spectrometers:

Varian UnityPlus 500 MHz
Varian UnityPlus 600 MHz

UNP	Q9BZB8
BMRB	19771
PDB	2M13 2MKE
DBJ	BAB14496 BAB33089 BAC37017 BAG63194 BAH11723
EMBL	CAA69588 CAH92427
GB	AAH35348 AAH50629 AAI25477 AAK01239 AAK01240
REF	NP_001073001 NP_001073002 NP_001073003 NP_001099746 NP_001126432
SP	P0C279 P70166 Q5R733 Q9BZB8
TPG	DAA17635
AlphaFold	Q9H8V5 P0C279 P70166 Q5R733 Q9BZB8