BMRB Entry 25423

Name: Solution structure of NDP52 ubiquitin-binding zinc finger
Published: 2015-11-09

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PDB ID: 2mxp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25423
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: Solution structure of NDP52 ubiquitin-binding zinc finger PubMed: 26506893

Deposition date: 2015-01-12 Original release date: 2015-11-09

Authors: Pan, Lifeng; Xie, Xingqiao

Citation: Xie, Xingqiao; Wang, Yingli; Lin, Zhijie; Chen, Xiaofang; Liu, Jianping; Pan, Lifeng. "Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2" Autophagy 11, 1775-1789 (2015).

Assembly members:
entity_1, polymer, 33 residues, 3887.567 Da.
ZINC ION, non-polymer, 65.409 Da.

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

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

Entity Sequences (FASTA):
entity_1: QMQPLCFNCPICDKIFPATE KQIFEDHVFCHSL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	103
15N chemical shifts	34
1H chemical shifts	241

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	ZINC ION	2

Entities:

Entity 1, entity_1 33 residues - 3887.567 Da.

1

GLN

MET

GLN

PRO

LEU

CYS

PHE

ASN

CYS

PRO

2

ILE

CYS

ASP

LYS

ILE

PHE

PRO

ALA

THR

GLU

3

LYS

GLN

ILE

PHE

GLU

ASP

HIS

VAL

PHE

CYS

4

HIS

SER

LEU

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 1 mM; entity_1, [U-100% 15N], 1 mM; D2O 10%; H2O 90%; Potassium phosphate buffer 50 mM; NaCl 50 mM; DTT 1 mM

sample_2: entity_1, [U-100% 13C; U-100% 15N], 1 mM; D2O 100%; Potassium phosphate buffer 50 mM; NaCl 50 mM; DTT 1 mM

sample_3: entity_1 1.2 mM; D2O 100%; Potassium phosphate buffer 50 mM; NaCl 50 mM; DTT 1 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.1 M; pH: 6.5; pressure: 2 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_2

Software:

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

PIPP, Garrett - chemical shift assignment, data analysis

SPARKY, Goddard - chemical shift assignment, data analysis

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Agilent INOVA 800 MHz

PDB	2MXP 4XKL
DBJ	BAD96947 BAG37327 BAG56685 BAG56845 BAG60448
EMBL	CAG33044 CAH92289
GB	AAA75297 AAH04130 AAH15893 ADQ32739 ADZ15727
REF	NP_001126338 NP_001233315 NP_001248319 NP_001248320 NP_001248322
SP	Q13137 Q5R7H1

Biological Magnetic Resonance Data Bank