BMRB Entry 18570

Name: Solution structure of the zinc finger AFV1p06 protein from the hyperthermophilic archaeal virus AFV1
Published: 2013-01-28

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PDB ID: 2lvh
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18570
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of the zinc finger AFV1p06 protein from the hyperthermophilic archaeal virus AFV1

Deposition date:

2012-07-05

Original release date:

2013-01-28

Authors:

Guilliere, Florence; Sezonov, Guennadi; Prangishvili, David; Delepierre, Muriel; Guijarro, J. Inaki

Citation:

Citation: Guilliere, Florence; Danioux, Chloe; Jaubert, Carole; Desnoues, Nicole; Delepierre, Muriel; Prangishvili, David; Sezonov, Guennadi; Guijarro, J. Inaki. "Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold" PLoS One 8, e52908-e52908 (2013).
PubMed: 23326363

Assembly members:

Assembly members:
AFV1p06, polymer, 59 residues, 5437.367 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Acidianus Filamentous Virus 1 (AFV1) Taxonomy ID: 235266 Superkingdom: Viruses Kingdom: not available Genus/species: Gammalipothrixvirus Acidianus Filamentous Virus 1 (AFV1)

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-30a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
AFV1p06: MIEVSSMERVYQCLRCGLTF RTKKQLIRHLVNTEKVNPLS IDYYYQSFSVSLKDVNKII

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	271
15N chemical shifts	59
1H chemical shifts	434

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	zinc finger AFV1p06 protein	1
2	ZINC ION	2

Entities:

Entity 1, zinc finger AFV1p06 protein 59 residues - 5437.367 Da.

Residues 1-7 and 51-59 are disordered; only residues 7-51 are included in the structures

1

MET

ILE

GLU

VAL

SER

MET

GLU

ARG

VAL

2

TYR

GLN

CYS

LEU

ARG

CYS

GLY

LEU

THR

PHE

3

ARG

THR

LYS

GLN

LEU

ILE

ARG

HIS

LEU

4

VAL

ASN

THR

GLU

LYS

VAL

ASN

PRO

LEU

SER

5

ILE

ASP

TYR

GLN

SER

PHE

SER

VAL

6

SER

LEU

LYS

ASP

VAL

ASN

LYS

ILE

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: AFV1p06, [U-98% 13C; U-98% 15N], 0.8-1 mM; Na-HEPES 50 mM; NaCl 150 mM; ZnCl2 50 uM; DTT 3 mM

sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 298.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD aromatic	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCDCE)HE aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

VNMRJ v2.3A, Varian - collection

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

NMRView v5.3, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

ARIA v2.2, Linge, O'Donoghue and Nilges - Automated NOE assignment, structure solution

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution, water refinement

TALOS, Cornilescu, Delaglio and Bax - Dihedral constraints

Procheck v3.5.4, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho - Structure analysis

WhatCheck, Vriend - Structure analysis

Molmol v2K.2, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Varian NMR System 600 MHz

EMBL	Q70LE5 CAD98935
GB	YP_003731
PDB	2LVH
REF	YP_003731
SP	Q70LE5
AlphaFold	Q70LE5