PDB-6hag: The structure of the SAM/SAH-binding riboswitch.

ID or keywords:

Entry

Database: PDB / ID: 6hag

Title

The structure of the SAM/SAH-binding riboswitch.

Components

SAM Riboswitch

Keywords

RNA /

riboswitch / SAM / SAH /

pseudoknot

Function / homology

S-ADENOSYL-L-HOMOCYSTEINE /

RNA / RNA (> 10)

Function and homology information

Biological species

Proteobacteria (purple photosynthetic bacteria and relatives)

Method

SOLUTION NMR / torsion angle dynamics

Authors

Weickhmann, A.K.

Funding support

Germany, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2019
Title: The structure of the SAM/SAH-binding riboswitch.
Authors: Weickhmann, A.K. / Keller, H. / Wurm, J.P. / Strebitzer, E. / Juen, M.A. / Kremser, J. / Weinberg, Z. / Kreutz, C. / Duchardt-Ferner, E. / Wohnert, J.

History

Deposition	Aug 7, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 9, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2019	Group: Data collection / Database references / Category: citation / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	May 8, 2019	Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3	Jan 29, 2020	Group: Data collection / Database references / Category: database_2 / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6hag.cif.gz	315.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6hag.ent.gz	275.1 KB	Display	PDB format
PDBx/mmJSON format	6hag.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/6hag ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6hag	HTTPS FTP

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Related structure data

Similar structure data	3ivn-2 1y26-d 6p2h-d 4tzx-d 6e33-d 4fei-1 1t6v-1 2mhq-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	BMRB: 27452

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #10 - Oct 2000 Ribosome similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #161 - May 2013 Ricin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #227 - Nov 2018 Telomerase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (2)
#15 - Mar 2001
Transfer RNA
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: SAM Riboswitch

hetero molecules

14.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: isothermal titration calorimetry

NMR ensembles

	Data	Criteria
Number of conformers (submitted / calculated)	10 / 10	structures with the least restraint violations
Representative	Model #1	target function

#1: RNA chain	SAM Riboswitch Mass: 13833.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteobacteria (purple photosynthetic bacteria and relatives) Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S

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Experiment

Experiment

Method:

SOLUTION NMR

NMR experiment

Conditions-ID	Experiment-ID	Solution-ID	Sample state	Spectrometer-ID	Type
1	39	1	isotropic	5	2D 1H-15N HSQC
1	55	3	isotropic	4	2D 1H-15N HSQC
1	54	6	isotropic	3	2D 1H-15N HSQC
1	53	7	isotropic	3	2D 1H-15N HSQC
2	52	2	isotropic	5	2D 1H-15N HSQC NH2 only
2	51	1	isotropic	5	2D 1H-13C HSQC aliphatic
2	50	6	isotropic	5	2D 1H-13C HSQC aliphatic
2	49	3	isotropic	5	2D 1H-13C HSQC aliphatic
2	48	7	isotropic	5	2D 1H-13C HSQC aliphatic
2	47	1	isotropic	5	2D 1H-13C HSQC aromatic
2	46	6	isotropic	3	2D 1H-13C HSQC aromatic
2	45	3	isotropic	3	2D 1H-13C HSQC aromatic
2	44	7	isotropic	3	2D 1H-13C HSQC aromatic
3	43	8	isotropic	4	2D 1H-1H NOESY
2	42	6	isotropic	1	3D 1H-13C NOESY aromatic
2	41	3	isotropic	1	3D 1H-13C NOESY aromatic
2	40	7	isotropic	1	3D 1H-13C NOESY aromatic
2	57	9	isotropic	1	3D 1H-13C NOESY aliphatic3D 1H-13C NOESY aliphatic
2	56	10	isotropic	1	3D 1H-13C NOESY aliphatic
2	58	11	isotropic	1	3D 1H-13C NOESY aliphatic
3	59	8	isotropic	4	2D 1H-1H NOESY
2	60	9	isotropic	3	3D (H)CCH-TOCSY
2	61	9	isotropic	3	3D (H)CCH-COSY
2	62	10	isotropic	3	3D (H)CCH-TOCSY
2	63	10	isotropic	3	3D (H)CCH-COSY
2	64	11	isotropic	3	3D (H)CCH-TOCSY
2	65	11	isotropic	3	3D (H)CCH-COSY
1	66	8	isotropic	4	1D 1H-HS11ECHO
1	67	1	isotropic	3	2D 1H-15N HNN-COSY
2	68	7	isotropic	3	2D 1H-13C HNCO
2	69	3	isotropic	3	2D 1H-13C HNCO
2	70	6	isotropic	3	2D 1H-13C H5C5(C4N)H
2	71	3	isotropic	3	2D 1H-15N HCN aromatic
2	72	10	isotropic	3	2D 1H-15N HCN aliphatic
2	73	2	isotropic	3	2D 1H-15N 2bond-HSQC
2	74	9	isotropic	2	TROSY relayed (H)CCH-COSY
2	75	7	isotropic	2	2D 1H-13C long-rangeH8(C8)C5(N1)H1
2	76	3	isotropic	3	2D 1H-13C H5C5(C4N)H
2	77	6	isotropic	3	2D 1H-15N HCN aromatic
2	78	9	isotropic	3	2D 1H-15N HCN aliphatic
2	79	7	isotropic	3	2D 1H-15N HCN aromatic
2	80	11	isotropic	3	2D 1H-15N HCN aliphatic
1	81	12	isotropic	1	2D 1H-15N HNN-COSY
3	82	2	isotropic	4	2D 1H-15N HSQC
2	83	2	isotropic	3	2D lr-1H,15N-HSQC
2	84	5	isotropic	1	2D 1H-13C HSQC aliphatic
2	85	5	isotropic	1	2D 1H-13C HSQC aromatic
2	86	5	isotropic	1	3D (H)CCH-COSY

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Sample preparation

Details

Type	Solution-ID	Contents	Label	Solvent system
solution	1	710 uM [U-13C; U-15N] env9b, 2 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 90% H2O/10% D2O	13C15N	90% H2O/10% D2O
solution	2	910 uM [U-15N] env9b, 2.5 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 90% H2O/10% D2O	15N	90% H2O/10% D2O
solution	3	800 uM [U-13C; U-15N]-Ura env9b, 1.6 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 90% H2O/10% D2O	13C15N-U	90% H2O/10% D2O
solution	4	750 saturated [U-5-D1/ribose-3 ,4 ,5 ,5 -D4] env9b, 3 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 90% H2O/10% D2O	seldeut	90% H2O/10% D2O
solution	5	700 uM env9b, 0.5 mM [U-13C; U-15N] S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 90% H2O/10% D2O	13C15N-SAH	90% H2O/10% D2O
solution	6	800 uM [U-13C; U-15N]-Cyt, [U-13C; U-15N]-Ade env9b, 2 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 90% H2O/10% D2O	13C15N-AC	90% H2O/10% D2O
solution	7	850 uM [U-13C; U-15N]-Gua env9b, 2 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 50% H2O/50% D2O	13C15N-G	50% H2O/50% D2O
solution	8	1.2 mM env9b, 4 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 90% H2O/10% D2O	unlab	90% H2O/10% D2O
solution	9	800 uM [U-13C; U-15N]-Cyt, [U-13C; U-15N]-Ade env9b, 2 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 100% D2O	13C15N-AC_D2O	100% D2O
solution	10	800 uM [U-13C; U-15N]-Ura env9b, 1.6 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 100% D2O	13C15N-U_D2O	100% D2O
solution	11	850 uM [U-13C; U-15N]-Gua env9b, 2 mM S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 100% D2O	13C15N-G_D2O	100% D2O
solution	12	480 uM [U-13C; U-15N]-Ura env9b, 750 uM [U-13C; U-15N] S-Adenosylhomocysteine, 25 mM potassium phosphate, 50 mM potassium chloride, 2 mM magnesium acetate, 100% D2O	13C15N-U,13C15N-SAH	100% D2O

Sample

Conc. (mg/ml)	Component	Isotopic labeling	Solution-ID
710 uM	env9b	[U-13C; U-15N]	1
2 mM	S-Adenosylhomocysteine	natural abundance	1
25 mM	potassium phosphate	natural abundance	1
50 mM	potassium chloride	natural abundance	1
2 mM	magnesium acetate	natural abundance	1
910 uM	env9b	[U-15N]	2
2.5 mM	S-Adenosylhomocysteine	natural abundance	2
25 mM	potassium phosphate	natural abundance	2
50 mM	potassium chloride	natural abundance	2
2 mM	magnesium acetate	natural abundance	2
800 uM	env9b	[U-13C; U-15N]-Ura	3
1.6 mM	S-Adenosylhomocysteine	natural abundance	3
25 mM	potassium phosphate	natural abundance	3
50 mM	potassium chloride	natural abundance	3
2 mM	magnesium acetate	natural abundance	3
750 saturated	env9b	[U-5-D1/ribose-3 ,4 ,5 ,5 -D4]	4
3 mM	S-Adenosylhomocysteine	natural abundance	4
25 mM	potassium phosphate	natural abundance	4
50 mM	potassium chloride	natural abundance	4
2 mM	magnesium acetate	natural abundance	4
700 uM	env9b	natural abundance	5
0.5 mM	S-Adenosylhomocysteine	[U-13C; U-15N]	5
25 mM	potassium phosphate	natural abundance	5
50 mM	potassium chloride	natural abundance	5
2 mM	magnesium acetate	natural abundance	5
800 uM	env9b	[U-13C; U-15N]-Cyt, [U-13C; U-15N]-Ade	6
2 mM	S-Adenosylhomocysteine	natural abundance	6
25 mM	potassium phosphate	natural abundance	6
50 mM	potassium chloride	natural abundance	6
2 mM	magnesium acetate	natural abundance	6
850 uM	env9b	[U-13C; U-15N]-Gua	7
2 mM	S-Adenosylhomocysteine	natural abundance	7
25 mM	potassium phosphate	natural abundance	7
50 mM	potassium chloride	natural abundance	7
2 mM	magnesium acetate	natural abundance	7
1.2 mM	env9b	natural abundance	8
4 mM	S-Adenosylhomocysteine	natural abundance	8
25 mM	potassium phosphate	natural abundance	8
50 mM	potassium chloride	natural abundance	8
2 mM	magnesium acetate	natural abundance	8
800 uM	env9b	[U-13C; U-15N]-Cyt, [U-13C; U-15N]-Ade	9
2 mM	S-Adenosylhomocysteine	natural abundance	9
25 mM	potassium phosphate	natural abundance	9
50 mM	potassium chloride	natural abundance	9
2 mM	magnesium acetate	natural abundance	9
800 uM	env9b	[U-13C; U-15N]-Ura	10
1.6 mM	S-Adenosylhomocysteine	natural abundance	10
25 mM	potassium phosphate	natural abundance	10
50 mM	potassium chloride	natural abundance	10
2 mM	magnesium acetate	natural abundance	10
850 uM	env9b	[U-13C; U-15N]-Gua	11
2 mM	S-Adenosylhomocysteine	natural abundance	11
25 mM	potassium phosphate	natural abundance	11
50 mM	potassium chloride	natural abundance	11
2 mM	magnesium acetate	natural abundance	11
480 uM	env9b	[U-13C; U-15N]-Ura	12
750 uM	S-Adenosylhomocysteine	[U-13C; U-15N]	12
25 mM	potassium phosphate	natural abundance	12
50 mM	potassium chloride	natural abundance	12
2 mM	magnesium acetate	natural abundance	12

Sample conditions

Conditions-ID	Ionic strength	Label	pH	Pressure (kPa)	Temperature (K)
1	50 mM	283	6.2	1 atm	283 K
2	50 mM	298	6.2	1 atm	298 K
3	50 mM	271	6.2	1 atm	271 K

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NMR measurement

NMR spectrometer

Type	Manufacturer	Model	Field strength (MHz)	Spectrometer-ID
Bruker AVANCE	Bruker	AVANCE	950	1
Bruker AVANCE	Bruker	AVANCE	900	2
Bruker AVANCE	Bruker	AVANCE	800	3
Bruker AVANCE	Bruker	AVANCE	700	4
Bruker AVANCE	Bruker	AVANCE	600	5

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Processing

NMR software

Name	Version	Developer	Classification
CYANA	3.97	Guntert, Mumenthaler and Wuthrich	refinement
CYANA	3.97	Guntert, Mumenthaler and Wuthrich	structure calculation
TopSpin		Bruker Biospin	data analysis
CARA		Keller and Wuthrich	chemical shift assignment
CARA		Keller and Wuthrich	peak picking

Refinement

Method: torsion angle dynamics / Software ordinal: 1

NMR representative

Selection criteria: target function

NMR ensemble

Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 10 / Conformers submitted total number: 10

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