BMRB Entry 18863

Name: The Solution Structure of Monomeric Hepatitis C Virus p7 Yields Potent Inhibitors of Virion Release
Published: 2013-08-26

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PDB ID: 3zd0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18863
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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 Solution Structure of Monomeric Hepatitis C Virus p7 Yields Potent Inhibitors of Virion Release

Deposition date:

2012-11-27

Original release date:

2013-08-26

Authors:

Thompson, Gary; Kalverda, Arnout; Griffin, Steven; Foster, Toshana; Sthompson, G.; Kankanala, Jayakanth; Thompson, Joseph; Barker, Amy; Clarke, Dean; Noerenberg, Marko; Pearson, Arwen; Rowlands, David; Homans, Steve; Harris, Mark; Foster, Richard

Citation:

Citation: Foster, Toshana; Thompson, Gary; Kalverda, Arnout; Kankanala, Jayakanth; Bentham, Matthew; Wetherill, Laura; Thompson, Joseph; Barker, Amy; Clarke, Dean; Noerenberg, Marko; Pearson, Arwen; Rowlands, David; Homans, Steven; Harris, Mark; Foster, Richard; Griffin, Stephen. "Structure-guided design affirms inhibitors of hepatitis C virus p7 as a viable class of antivirals targeting virion release." Hepatology 59, 408-422 (2014).
PubMed: 24022996

Assembly members:

Assembly members:
p7, polymer, 86 residues, 9058.5093 Da.

Natural source:

Natural source: Common Name: Hepatitis C virus Taxonomy ID: 11103 Superkingdom: Viruses Kingdom: not available Genus/species: Hepacivirus Hepatitis C virus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PGEX-FLAGP7(J4)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
p7: GPLGSPEFAAMDYKDDDDKA LENLVVLNAASVAGAHGILS FLVFFCAAWYIKGRLAPGAA YAFYGVWPLLLLLLALPPRA YAAAAS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list
spectral_peak_list

Data type	Count
13C chemical shifts	278
15N chemical shifts	78
1H chemical shifts	412

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	p7	1

Entities:

Entity 1, p7 86 residues - 9058.5093 Da.

1

GLY

PRO

LEU

GLY

SER

PRO

GLU

PHE

ALA

2

MET

ASP

TYR

LYS

ASP

LYS

ALA

3

LEU

GLU

ASN

LEU

VAL

LEU

ASN

ALA

4

SER

VAL

ALA

GLY

ALA

HIS

GLY

ILE

LEU

SER

5

PHE

LEU

VAL

PHE

CYS

ALA

TRP

TYR

6

ILE

LYS

GLY

ARG

LEU

ALA

PRO

GLY

ALA

7

TYR

ALA

PHE

TYR

GLY

VAL

TRP

PRO

LEU

8

LEU

ALA

LEU

PRO

ARG

ALA

9

TYR

ALA

SER

Samples:

methanol_H: p7 0.0005 ± 0.0001 mol/mol

methanol_CN: p7, [U-100% 13C; U-100% 15N], 0.0005 ± 0.0001 mol/mol

methanol_N: p7, [U-100% 15N], 0.0005 ± 0.0001 mol/mol

methanol_25c: ionic strength: 0.000 M; pH: 0.000; pressure: 1.000 atm; temperature: 298.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	methanol_CN	isotropic	methanol_25c
2D 1H-15N HSQC/HMQC	methanol_CN	isotropic	methanol_25c
3D HN(CO)CA	methanol_CN	isotropic	methanol_25c
3D HNCACB	methanol_CN	isotropic	methanol_25c
3D CBCA(CO)NH	methanol_CN	isotropic	methanol_25c
3D HNCO	methanol_CN	isotropic	methanol_25c
hCcacoNH (hC_cacoNH.relayed)	methanol_CN	isotropic	methanol_25c
3D H(CCO)NH	methanol_CN	isotropic	methanol_25c
HNHA (H{[N]+[HA]})	methanol_N	isotropic	methanol_25c
3D HCCH-COSY	methanol_CN	isotropic	methanol_25c
hCCHtocsy (hC_CH.relayed)	methanol_CN	isotropic	methanol_25c
2D 1H-13C HSQC/HMQC	methanol_CN	isotropic	methanol_25c
3D HCCH-TOCSY	methanol_CN	isotropic	methanol_25c
2D 1H-1H TOCSY	methanol_H	isotropic	methanol_25c
2D 1H-1H NOESY	methanol_H	isotropic	methanol_25c
2D 1H-1H NOESY	methanol_H	isotropic	methanol_25c
hbCBcgcdHD (hbCBcgcdHD)	methanol_CN	isotropic	methanol_25c
2D 1H-13C HSQC/HMQC	methanol_CN	isotropic	methanol_25c
13C_HSQC_HCcaro (H[C[caro]])	methanol_CN	isotropic	methanol_25c
3D 1H-15N NOESY	methanol_N	isotropic	methanol_25c
13C_HSQC_HCCARO	methanol_CN	solution	methanol_25c
15N_HSQC	methanol_CN	solution	methanol_25c
HNCA	methanol_CN	solution	methanol_25c

Software:

ARIA v2.2u3, Nilges group, Institute Pasteur - structure calculation nOe assignment

AutoDep v4.3, PDBe - collection

CNS v1.1, CNS Developers - molecular synamics

ANALYSIS v2.2, CCPN - deposition

MEMBRANE_CS_ROSETTA-ARIA_2-2U3-CNS vany, Linge, O'Donoghue and Nilges - data analysis

Rosetta_3 v3, rosetta commons/ baker lab - structure calculation

TALOS v2007.068.09.0, bax group - secondary structure

CS-Rosetta v1.01, bax group - structure calculation

NMR spectrometers:

Varian UnityInova 600 MHz
Varian UnityInova 750 MHz
Varian UnityInova 500 MHz

UNP	Q9WLK8_9HEPC
BMRB	25178 25181
PDB	2MTS 3ZD0
DBJ	BAA01583 BAA02756
EMBL	CAH23571 CAH23600 CAK19390 CDU41873 CDU41874
GB	AAC15722 AAC15723 AAC15724 AAC15725 AAC15726
SP	O92972
AlphaFold	Q9WLK8 O92972