BMRB Entry 34465

Name: Structure of a protein-RNA complex by ssNMR
Published: 2020-02-06

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PDB ID: 6tph
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR34465
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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:

Structure of a protein-RNA complex by ssNMR

Deposition date:

2019-12-13

Original release date:

2020-02-06

Authors:

Mumdooh, A.; Marchanka, A.; Carlomagno, T.

Citation:

Citation: Ahmed, M.; Marchanka, A.; Carlomagno, T.. "Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy" Angew. Chem. Int. Ed. Engl. 59, 6866-6873 (2020).
PubMed: 32023357

Assembly members:

Assembly members:
entity_1, polymer, 123 residues, 13414.664 Da.
entity_2, polymer, 26 residues, 8407.075 Da.

Natural source:

Natural source: Common Name: Pyrococcus furiosus Taxonomy ID: 2261 Superkingdom: Archaea Kingdom: not available Genus/species: Pyrococcus furiosus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MAKPSYVKFEVPKELAEKAL QAVEIARDTGKIRKGTNETT KAVERGQAKLVIIAEDVDPE EIVAHLPPLCEEKEIPYIYV PSKKELGAAAGIEVAAASVA IIEPGKARDLVEEIAMKVKE LMK
entity_2: GCUGAGCUCGAAAGAGCAAU GAUGUC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	327
15N chemical shifts	98

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	entity_2	2

Entities:

Entity 1, entity_1 123 residues - 13414.664 Da.

1

MET

ALA

LYS

PRO

SER

TYR

VAL

LYS

PHE

GLU

2

VAL

PRO

LYS

GLU

LEU

ALA

GLU

LYS

ALA

LEU

3

GLN

ALA

VAL

GLU

ILE

ALA

ARG

ASP

THR

GLY

4

LYS

ILE

ARG

LYS

GLY

THR

ASN

GLU

THR

5

LYS

ALA

VAL

GLU

ARG

GLY

GLN

ALA

LYS

LEU

6

VAL

ILE

ALA

GLU

ASP

VAL

ASP

PRO

GLU

7

GLU

ILE

VAL

ALA

HIS

LEU

PRO

LEU

CYS

8

GLU

LYS

GLU

ILE

PRO

TYR

ILE

TYR

VAL

9

PRO

SER

LYS

GLU

LEU

GLY

ALA

10

GLY

ILE

GLU

VAL

ALA

SER

VAL

ALA

11

ILE

GLU

PRO

GLY

LYS

ALA

ARG

ASP

LEU

12

VAL

GLU

ILE

ALA

MET

LYS

VAL

LYS

GLU

13

LEU

MET

LYS

Entity 2, entity_2 26 residues - 8407.075 Da.

1

G

C

U

G

A

G

C

U

C

G

2

A

G

A

G

C

A

U

3

G

A

U

G

U

C

Samples:

sample_1: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_2: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 8 mg/mL; RNA (26-MER) 5 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_3: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; RNA (26-MER) 10 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 12 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_4: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ade), [U-13C; U-15N]-Ade, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_5: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ura), [U-13C; U-15N]-Ura, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_6: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; RNA (26-MER) 10 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 12 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_7: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ade), [U-13C; U-15N]-Ade, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_8: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ura), [U-13C; U-15N]-Ura, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_9: 50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N), [U-99% 13C; U-99% 15N], 4 mg/mL; RNA (26-MER) 10 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 12 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_10: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ade), [U-13C; U-15N]-Ade, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_11: RNA (26-MER) 8 mg/mL; 50S RIBOSOMAL PROTEIN L7AE 16 mg/mL; RNA (26-MER) (U-13C, U-15N-ura), [U-13C; U-15N]-Ura, 2 mg/mL; HEPES 25 mM; NaCl 120 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.6; pressure: 1 bar; temperature: 265 K

sample_conditions_2: ionic strength: 150 mM; pH: 7.6; pressure: 1 bar; temperature: 260 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NCA	sample_1	anisotropic	sample_conditions_1
2D NCO	sample_1	anisotropic	sample_conditions_1
2D 13C,13C DARR	sample_1	anisotropic	sample_conditions_1
3D NCACX	sample_2	anisotropic	sample_conditions_1
3D NCOCX	sample_2	anisotropic	sample_conditions_1
2D 13C,13C DARR	sample_2	anisotropic	sample_conditions_1
3D CANCO	sample_2	anisotropic	sample_conditions_1
2D 13C,13C SPC53	sample_2	anisotropic	sample_conditions_1
2D 13C,13C SPC53	sample_3	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_4	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_6	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_5	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_7	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_8	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_9	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_10	anisotropic	sample_conditions_2
2D 13C,13C SPC53	sample_11	anisotropic	sample_conditions_2

Software:

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

HADDOCK, Bonvin - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

TopSpin, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE III 600 MHz