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- PDB-6tph: Structure of a protein-RNA complex by ssNMR -

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Basic information

Entry
Database: PDB / ID: 6tph
TitleStructure of a protein-RNA complex by ssNMR
Components
  • 50S ribosomal protein L7Ae
  • RNA (26-MER)
KeywordsRNA / solid-state RNA / protein-RNA complex / structure determination / PRE
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / rRNA processing / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodSOLID-STATE NMR / na
AuthorsMumdooh, A. / Marchanka, A. / Carlomagno, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CA294/10-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy.
Authors: Ahmed, M. / Marchanka, A. / Carlomagno, T.
History
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L7Ae
B: RNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)21,8222
Polymers21,8222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1210 Å2
ΔGint-10 kcal/mol
Surface area9900 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein 50S ribosomal protein L7Ae / Large ribosomal subunit protein eL8 / Ribosomal protein L8e


Mass: 13414.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae, PF1367 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U160
#2: RNA chain RNA (26-MER)


Mass: 8407.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription / Source: (synth.) Pyrococcus furiosus (archaea)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D NCA
121anisotropic12D NCO
131anisotropic12D 13C,13C DARR
142anisotropic13D NCACX
152anisotropic13D NCOCX
172anisotropic13D CANCO
162anisotropic12D 13C,13C DARR
182anisotropic12D 13C,13C SPC53
293anisotropic12D 13C,13C SPC53
2104anisotropic12D 13C,13C SPC53
2125anisotropic12D 13C,13C SPC53
2116anisotropic12D 13C,13C SPC53
2137anisotropic12D 13C,13C SPC53
2148anisotropic12D 13C,13C SPC53
2159anisotropic12D 13C,13C SPC53
21610anisotropic12D 13C,13C SPC53
21711anisotropic12D 13C,13C SPC53

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid14 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, solidu-13C,15N L7Ae for CSPL7Aesolid
solid28 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 5 mg/mL RNA (26-MER), solidu-13C,15N-L7Ae-N.A.-26mer RNA for assignmentL7Ae-RNAsolid
solid34 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 12 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 10 mg/mL RNA (26-MER), solidu-13C,15N-SL-K32-L7Ae-N.A.-26mer RNA for PRE ruler determinationSL-L7Ae-K32C-RNAsolid
solid416 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ade RNA (26-MER), 8 mg/mL RNA (26-MER), solidN.A-SL-K32C-L7Ae-Alab-26mer RNA for PRE measurementsSL-L7Ae-K32C-Alab-RNAsolid
solid516 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ura RNA (26-MER), 8 mg/mL RNA (26-MER), solidN.A-SL-K32C-L7Ae-Ulab-26mer RNA for PRE measurementsSL-L7Ae-K32C-Ulab-RNAsolid
solid64 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 12 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 10 mg/mL RNA (26-MER), solidu-13C,15N-SL-N38C-L7Ae-N.A.-26mer RNA for PRE ruler determinationSL-L7Ae-N38C-RNAsolid
solid716 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ade RNA (26-MER), 8 mg/mL RNA (26-MER), solidN.A-SL-N38C-L7Ae-Alab-26mer RNA for PRE measurementsSL-L7Ae-N38C-Alab-RNAsolid
solid816 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ura RNA (26-MER), 8 mg/mL RNA (26-MER), solidN.A-SL-N38C-L7Ae-Ulab-26mer RNA for PRE measurementsSL-L7Ae-N38C-Ulab-RNAsolid
solid94 mg/mL [U-99% 13C; U-99% 15N] 50S RIBOSOMAL PROTEIN L7AE, 12 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 10 mg/mL RNA (26-MER), solidu-13C,15N-SL-N38C-L7Ae-N.A.-26mer RNA for PRE ruler determinationSL-L7Ae-I93C-RNAsolid
solid1016 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ade RNA (26-MER), 8 mg/mL RNA (26-MER), solidN.A-SL-I93C-L7Ae-Alab-26mer RNA for PRE measurementsSL-L7Ae-I93C-Alab-RNAsolid
solid1116 mg/mL 50S RIBOSOMAL PROTEIN L7AE, 2 mg/mL [U-13C; U-15N]-Ura RNA (26-MER), 8 mg/L RNA (26-MER), solidN.A-SL-I93C-L7Ae-Ulab-26mer RNA for PRE measurementsSL-L7Ae-I93C-Ulab-RNAsolid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mg/mL50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N)[U-99% 13C; U-99% 15N]1
8 mg/mL50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N)[U-99% 13C; U-99% 15N]2
5 mg/mLRNA (26-MER)natural abundance2
4 mg/mL50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N)[U-99% 13C; U-99% 15N]3
12 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance3
10 mg/mLRNA (26-MER)natural abundance3
16 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance4
2 mg/mLRNA (26-MER) (U-13C, U-15N-ade)[U-13C; U-15N]-Ade4
8 mg/mLRNA (26-MER)natural abundance4
16 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance5
2 mg/mLRNA (26-MER) (U-13C, U-15N-ura)[U-13C; U-15N]-Ura5
8 mg/mLRNA (26-MER)natural abundance5
4 mg/mL50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N)[U-99% 13C; U-99% 15N]6
12 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance6
10 mg/mLRNA (26-MER)natural abundance6
16 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance7
2 mg/mLRNA (26-MER) (U-13C, U-15N-ade)[U-13C; U-15N]-Ade7
8 mg/mLRNA (26-MER)natural abundance7
16 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance8
2 mg/mLRNA (26-MER) (U-13C, U-15N-ura)[U-13C; U-15N]-Ura8
8 mg/mLRNA (26-MER)natural abundance8
4 mg/mL50S RIBOSOMAL PROTEIN L7AE (U-13C, U-15N)[U-99% 13C; U-99% 15N]9
12 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance9
10 mg/mLRNA (26-MER)natural abundance9
16 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance10
2 mg/mLRNA (26-MER) (U-13C, U-15N-ade)[U-13C; U-15N]-Ade10
8 mg/mLRNA (26-MER)natural abundance10
16 mg/mL50S RIBOSOMAL PROTEIN L7AEnatural abundance11
2 mg/mLRNA (26-MER) (U-13C, U-15N-ura)[U-13C; U-15N]-Ura11
8 mg/mLRNA (26-MER)natural abundance11
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1solid-state sample, amount of sample in mg is given in samples description150 mML7Ae_assignment7.6 1 bar265 K
2solid-state sample, amount of sample in mg is given in samples description150 mMPRE_measurements7.6 1 bar260 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: 3.2 mm HCN MAS

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
HADDOCKBonvinstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpinBruker Biospincollection
RefinementMethod: na / Software ordinal: 1
Details: 10 structures with best haddock score were subjected to 15 ns of MD simulation.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10

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