BMRB Entry 52654

Name: Solid-state NMR assignment of membrane-embedded SARS-CoV-2 ORF6 accessory protein
Published: 2025-05-21

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52654

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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:

Solid-state NMR assignment of membrane-embedded SARS-CoV-2 ORF6 accessory protein

Deposition date:

2024-10-24

Original release date:

2025-05-21

Authors:

Ninot Pedrosa, Marti; Palfy, Gyula; Bockmann, Anja; Meier, Beat; Lecoq, Lauriane

Citation:

Citation: Ninot Pedrosa, Marti; Palfy, Gyula; Razmazma, Hafez; Crowley, Jackson; Fogeron, Marie-Laure; Bersch, Beate; Barnes, Alexander; Brutscher, Bernhard; Monticelli, Luca; Bockmann, Anja; Meier, Beat; Lecoq, Lauriane. "NMR structure of SARS-CoV-2 ORF6 reveals an N-terminal membrane anchor" J. Am. Chem. Soc. ., .-..

Assembly members:

Assembly members:
SARS-CoV-2 ORF6, polymer, 62 residues, 7330 Da.

Natural source:

Natural source: Common Name: SARS-CoV-2 Taxonomy ID: 2697049 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus HCoV-SARS

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: wheat germ - cell free Vector: pEU-E01-MCS

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SARS-CoV-2 ORF6: MFHLVDFQVTIAEILLIIMR TFKVSIWNLDYIINLIIKNL SKSLTENKYSQLDEEQPMEI DG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	93
15N chemical shifts	32
1H chemical shifts	183

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ORF6	1

Entities:

Entity 1, ORF6 62 residues - 7330 Da.

Additional glycine at the end of the original sequence

1

MET

PHE

HIS

LEU

VAL

ASP

PHE

GLN

VAL

THR

2

ILE

ALA

GLU

ILE

LEU

ILE

MET

ARG

3

THR

PHE

LYS

VAL

SER

ILE

TRP

ASN

LEU

ASP

4

TYR

ILE

ASN

LEU

ILE

LYS

ASN

LEU

5

SER

LYS

SER

LEU

THR

GLU

ASN

LYS

TYR

SER

6

GLN

LEU

ASP

GLU

GLN

PRO

MET

GLU

ILE

7

ASP

GLY

Samples:

sample_1: ORF6, [U-13C; U-15N]-Ala,Arg,Lys,Thr,Val, 1 mg; DSS 0.035 % v/v; HEPES 50 mM; ERGIC-PI4P lipid membrane 1 mg; sodium chloride 100 mM; TCEP 1 mM

sample_2: ORF6, [U-13C; U-15N]-Phe,Leu,Ala,Thr,Asp (other amino acids deuterated), 1.2 mg; DSS 0.035 % v/v; HEPES 50 mM; ERGIC-PI4P lipid membrane 0.8 mg; sodium chloride 100 mM; TCEP 1 mM

sample_3: ORF6, [U-13C; U-15N]-His,Ala,Asn,Gly,Tyr,Trp,Glu (other amino acids deuterated), 1.2 mg; DSS 0.035 % v/v; HEPES 50 mM; ERGIC-PI4P lipid membrane 0.8 mg; sodium chloride 100 mM; TCEP 1 mM

sample_4: ORF6, [U-13C; U-15N]-Ser,Ile,Met,Pro,Ala,Gln (other amino acids deuterated), 1.2 mg; DSS 0.035 % v/v; HEPES 50 mM; ERGIC-PI4P lipid membrane 0.8 mg; sodium chloride 100 mM; TCEP 1 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7.4; pressure: 1 atm; temperature: 281 K

sample_conditions_2: ionic strength: 125 mM; pH: 7.4; pressure: 1 atm; temperature: 297 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-detected CP-based SAFR-hCH	sample_1	isotropic	sample_conditions_1
1H-detected CP-based SAFR-hNH	sample_1	isotropic	sample_conditions_1
1H-detected CP-based SAFR-hCCH	sample_1	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNCAH	sample_1	isotropic	sample_conditions_2
1H-detected SAFR hCH refocused INEPT	sample_1	isotropic	sample_conditions_2
1H-detected CP-based SAFR hCoNH	sample_1	isotropic	sample_conditions_2
1H-detected SAFR hNH refocused INEPT	sample_1	isotropic	sample_conditions_1
1H-detected CP-based SAFR-hCANH	sample_1	isotropic	sample_conditions_2
1H-detected SAFR CP-based hNcoCAH	sample_1	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCH	sample_1	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNH	sample_1	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCH	sample_2	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNH	sample_2	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCCH	sample_2	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNCAH	sample_2	isotropic	sample_conditions_2
1H-detected SAFR hCH refocused INEPT	sample_2	isotropic	sample_conditions_2
1H-detected CP-based SAFR hCoNH	sample_2	isotropic	sample_conditions_1
1H-detected SAFR hNH refocused INEPT	sample_2	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCANH	sample_2	isotropic	sample_conditions_1
1H-detected CP-based SAFR-hCH	sample_2	isotropic	sample_conditions_1
1H-detected CP-based SAFR-hNH	sample_2	isotropic	sample_conditions_1
1H-detected CP-based SAFR-hCH	sample_3	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNH	sample_3	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCCH	sample_3	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNCAH	sample_3	isotropic	sample_conditions_2
1H-detected SAFR hCH refocused INEPT	sample_3	isotropic	sample_conditions_2
1H-detected SAFR hNH refocused INEPT	sample_3	isotropic	sample_conditions_2
1H-detected CP-based SAFR hCoNH	sample_3	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCANH	sample_3	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCH	sample_4	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNH	sample_4	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCCH	sample_4	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hNCAH	sample_4	isotropic	sample_conditions_2
1H-detected SAFR hCH refocused INEPT	sample_4	isotropic	sample_conditions_2
1H-detected SAFR hNH refocused INEPT	sample_4	isotropic	sample_conditions_2
1H-detected CP-based SAFR hCoNH	sample_4	isotropic	sample_conditions_2
1H-detected CP-based SAFR-hCANH	sample_4	isotropic	sample_conditions_2

Software:

TOPSPIN v3.5, 4.0.9 and 4.1 - Spectra recording

CcpNMR v3.2 - chemical shift assignment

NMRbox - data analysis

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III 850 MHz
Bruker AVANCE NEO 950 MHz
Bruker AVANCE NEO 1200 MHz