PDB-4gma: Crystal structure of the adenosylcobalamin riboswitch

ID or keywords:

Entry

Database: PDB / ID: 4gma

Title

Crystal structure of the adenosylcobalamin riboswitch

Components

Adenosylcobalamin riboswitch

Keywords

RNA / adenosylcobalamin / riboswitch / AdoCbl

Function / homology

Adenosylcobalamin / RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

Marine metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 3.94 Å

Authors

Reyes, F.E. / Johnson, J.E. / Polaski, J.T. / Batey, R.T.

Citation

Journal: Nature / Year: 2012
Title: B12 cofactors directly stabilize an mRNA regulatory switch.
Authors: Johnson, J.E. / Reyes, F.E. / Polaski, J.T. / Batey, R.T.

History

Deposition	Aug 15, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2012	Group: Database references
Revision 1.2	Jun 28, 2017	Group: Data collection / Refinement description Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / software Item: _diffrn_radiation_wavelength.wavelength
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gma.cif.gz	227.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4gma.ent.gz	183.3 KB	Display	PDB format
PDBx/mmJSON format	4gma.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gma_validation.pdf.gz	929.1 KB	Display	wwPDB validaton report
Full document	4gma_full_validation.pdf.gz	936 KB	Display
Data in XML	4gma_validation.xml.gz	8.6 KB	Display
Data in CIF	4gma_validation.cif.gz	11 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gm/4gma ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gma	HTTPS FTP

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Related structure data

Related structure data	4frgC 4frnC C: citing same article (ref.)
Similar structure data	4g0r-d 2j69-1 2j69-2 5u0u-d 3mlx-d 1z14-d 2i15-d 5dqj-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (3) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #210 - Jun 2017 Adenine Riboswitch in Action similarity (2) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #10 - Oct 2000 Ribosome similarity (2) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (2) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #98 - Feb 2008 Small Interfering RNA similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #161 - May 2013 Ricin similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #227 - Nov 2018 Telomerase similarity (2) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #143 - Nov 2011 Toll-like Receptors 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) #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 (2)
#130 - Oct 2010
Riboswitches
similarity (3)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#260 - Aug 2021
Ribonuclease P
similarity (2)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (2)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
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#15 - Mar 2001
Transfer RNA
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#245 - May 2020
Spliceosomes
similarity (2)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
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)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

Z: Adenosylcobalamin riboswitch

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	96.648, 243.545, 87.102
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	21
Space group name H-M	C222

#1: RNA chain	Adenosylcobalamin riboswitch Mass: 68273.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was transcribed via in vitro T7 RNA polymerase / Source: (synth.) Marine metagenome (others)
#2: Chemical	ChemComp-B1Z / Adenosylcobalamin / Cobamamide Mass: 1580.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇₂H₁₀₁CoN₁₈O₁₇P / Comment: medication*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.1 Å³/Da / Density % sol: 69.9 %
Crystal grow	Temperature: 298 K / Method: hanging drop / pH: 7.5 Details: 10% isopropanol, 300 mM magnesium chloride, 100 mM sodium HEPES pH 7.5, hanging drop, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
4		1

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 0.97 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97 Å / Relative weight: 1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_sym value	D res high (Å)	D res low (Å)	Num. obs	% possible obs
7.2	1	4	15295	0.078	6.549	91.393	2131	95.8
3.6	2	4.9	7654	0.069	6.87	91.418	2121	95.7
3.6	3	5	6641	0.067	6.87	91.418	1847	95.4
3.7	4	7.6	32573	0.055	3.936	42.256	8743	93.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
20.69	88.37	87.9	1	0.043	0.043	6.3
14.63	20.69	94.5	1	0.044	0.044	6.8
11.94	14.63	94.8	1	0.056	0.056	6.7
10.34	11.94	95.4	1	0.08	0.08	7
9.25	10.34	95.3	1	0.117	0.117	7.1
8.45	9.25	96.3	1	0.164	0.164	7.3
7.82	8.45	96	1	0.225	0.225	7.3
7.31	7.82	96.7	1	0.321	0.321	7.4
6.9	7.31	97.2	1	0.377	0.377	7.4
6.54	6.9	96.8	1	0.595	0.595	7.3
20.69	91.39	87.9	2	0.033	0.033	3.2
14.63	20.69	94	2	0.046	0.046	3.4
11.94	14.63	94.4	2	0.056	0.056	3.4
10.34	11.94	94.9	2	0.077	0.077	3.5
9.25	10.34	95.1	2	0.117	0.117	3.6
8.45	9.25	96.3	2	0.158	0.158	3.7
7.82	8.45	96	2	0.215	0.215	3.6
7.31	7.82	96.7	2	0.334	0.334	3.7
6.9	7.31	97.2	2	0.374	0.374	3.7
6.54	6.9	96.5	2	0.615	0.615	3.7
20.69	91.42	87.9	3	0.035	0.035	3.2
14.63	20.69	94	3	0.044	0.044	3.4
11.94	14.63	93.5	3	0.061	0.061	3.4
10.34	11.94	94.3	3	0.078	0.078	3.5
9.25	10.34	95.3	3	0.117	0.117	3.6
8.45	9.25	96.3	3	0.164	0.164	3.7
7.82	8.45	96	3	0.213	0.213	3.7
7.31	7.82	96.7	3	0.327	0.327	3.7
6.9	7.31	97.2	3	0.398	0.398	3.8
6.54	6.9	98	3	0.472	0.472	3.3
12.45	42.26	73.1	4	0.034	0.034	3.5
8.8	12.45	89.9	4	0.035	0.035	3.5
7.19	8.8	90.1	4	0.044	0.044	3.6
6.22	7.19	92.2	4	0.049	0.049	3.7
5.57	6.22	92.4	4	0.06	0.06	3.7
5.08	5.57	94.5	4	0.078	0.078	3.7
4.7	5.08	94.5	4	0.107	0.107	3.8
4.4	4.7	95.8	4	0.186	0.186	3.8
4.15	4.4	96.1	4	0.232	0.232	3.8
3.94	4.15	96.1	4	0.404	0.404	3.8

Reflection

Resolution: 3.94→88.374 Å / Num. obs: 8706 / % possible obs: 99.4 % / Redundancy: 3.5 % / R_sym value: 0.048 / Net I/σ(I): 13.7

Reflection shell

Diffraction-ID: 1,2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
4.64-4.89	3.6	0.498	1.6	3067	855	0.498	99.9
4.89-5.19	3.6	0.287	2.7	2881	808	0.287	99.9
5.19-5.54	3.6	0.172	4.4	2759	767	0.172	100
5.54-5.99	3.5	0.113	6.4	2491	708	0.113	100
5.99-6.56	3.5	0.087	8.6	2335	664	0.087	99.8
6.56-7.34	3.5	0.055	13.6	2052	594	0.055	99.5
7.34-8.47	3.4	0.037	19.3	1769	526	0.037	99.6
8.47-10.37	3.3	0.029	19.2	1514	459	0.029	99.3
10.37-14.67	3.2	0.022	21.5	1175	367	0.022	98.8
14.67-88.374	2.9	0.02	30.4	535	184	0.02	87.5

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Phasing

Phasing MAD

D res high: 4.2 Å / D res low: 91.4 Å / FOM acentric: 0.307 / FOM centric: 0.242 / Reflection acentric: 6969 / Reflection centric: 1196

Phasing MAD set

Highest resolution: 4.2 Å / Lowest resolution: 91.4 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	1735	396
ISO_2	0.858	0.855	0.491	0.427	1730	354
ISO_3	0.824	0.897	0.504	0.425	1491	320
ISO_4	0.518	0.623	1.387	0.933	1699	344
ANO_1	0.791	0	1.152	0	1729	0
ANO_2	0.923	0	0.495	0	1593	0
ANO_3	0.959	0	0.459	0	1390	0
ANO_4	0.959	0	0.635	0	6779	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	11.79-91.4	0	0	0	0	270	115
ISO_1	8.37-11.79	0	0	0	0	528	117
ISO_1	6.85-8.37	0	0	0	0	709	127
ISO_1	5.93-6.85	0	0	0	0	228	37
ISO_1	5.31-5.93	0	0	0	0	0	0
ISO_1	4.85-5.31	0	0	0	0	0	0
ISO_1	4.49-4.85	0	0	0	0	0	0
ISO_1	4.2-4.49	0	0	0	0	0	0
ANO_1	11.79-91.4	0.581	0	1.846	0	270	0
ANO_1	8.37-11.79	0.78	0	1.383	0	528	0
ANO_1	6.85-8.37	0.949	0	0.638	0	705	0
ANO_1	5.93-6.85	0.989	0	0.375	0	226	0
ANO_1	5.31-5.93	0	0	0	0	0	0
ANO_1	4.85-5.31	0	0	0	0	0	0
ANO_1	4.49-4.85	0	0	0	0	0	0
ANO_1	4.2-4.49	0	0	0	0	0	0
ISO_2	11.79-91.4	1.017	0.796	0.808	0.551	270	106
ISO_2	8.37-11.79	0.726	0.788	0.636	0.42	527	107
ISO_2	6.85-8.37	0.855	0.992	0.271	0.222	709	109
ISO_2	5.93-6.85	0.941	1.115	0.167	0.175	224	32
ISO_2	5.31-5.93	0	0	0	0	0	0
ISO_2	4.85-5.31	0	0	0	0	0	0
ISO_2	4.49-4.85	0	0	0	0	0	0
ISO_2	4.2-4.49	0	0	0	0	0	0
ANO_2	11.79-91.4	0.784	0	0.97	0	248	0
ANO_2	8.37-11.79	0.896	0	0.571	0	489	0
ANO_2	6.85-8.37	0.975	0	0.254	0	649	0
ANO_2	5.93-6.85	0.992	0	0.171	0	207	0
ANO_2	5.31-5.93	0	0	0	0	0	0
ANO_2	4.85-5.31	0	0	0	0	0	0
ANO_2	4.49-4.85	0	0	0	0	0	0
ANO_2	4.2-4.49	0	0	0	0	0	0
ISO_3	11.79-91.4	0.895	0.899	0.848	0.489	268	104
ISO_3	8.37-11.79	0.736	0.847	0.571	0.422	526	108
ISO_3	6.85-8.37	0.853	0.948	0.244	0.227	697	108
ISO_3	5.93-6.85	0	0	0	0	0	0
ISO_3	5.31-5.93	0	0	0	0	0	0
ISO_3	4.85-5.31	0	0	0	0	0	0
ISO_3	4.49-4.85	0	0	0	0	0	0
ISO_3	4.2-4.49	0	0	0	0	0	0
ANO_3	11.79-91.4	0.883	0	0.783	0	251	0
ANO_3	8.37-11.79	0.963	0	0.502	0	490	0
ANO_3	6.85-8.37	0.988	0	0.225	0	649	0
ANO_3	5.93-6.85	0	0	0	0	0	0
ANO_3	5.31-5.93	0	0	0	0	0	0
ANO_3	4.85-5.31	0	0	0	0	0	0
ANO_3	4.49-4.85	0	0	0	0	0	0
ANO_3	4.2-4.49	0	0	0	0	0	0
ISO_4	11.79-91.4	0.773	0.854	0.994	0.709	243	86
ISO_4	8.37-11.79	0.848	0.985	0.906	0.605	523	110
ISO_4	6.85-8.37	0.87	0.94	0.608	0.448	705	120
ISO_4	5.93-6.85	0.761	0.867	0.486	0.341	228	28
ISO_4	5.31-5.93	0	0	0	0	0	0
ISO_4	4.85-5.31	0	0	0	0	0	0
ISO_4	4.49-4.85	0	0	0	0	0	0
ISO_4	4.2-4.49	0	0	0	0	0	0
ANO_4	11.79-91.4	0.962	0	0.302	0	236	0
ANO_4	8.37-11.79	0.929	0	0.503	0	496	0
ANO_4	6.85-8.37	0.904	0	0.652	0	687	0
ANO_4	5.93-6.85	0.948	0	0.702	0	844	0
ANO_4	5.31-5.93	0.975	0	0.796	0	968	0
ANO_4	4.85-5.31	0.99	0	0.805	0	1106	0
ANO_4	4.49-4.85	1	0	0.772	0	1211	0
ANO_4	4.2-4.49	1.019	0	0.828	0	1231	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	24.608	-61.553	24.398	TA	200	0.08
2	24.608	-61.553	24.398	BR	200	0.03
3	10.391	23.153	25.997	CO	200	0.94
4	58.513	83.333	77.096	TA	200	0.1
5	58.513	83.333	77.096	BR	200	0.05
6	73.824	184.658	69.025	TA	200	0.02
7	73.824	184.658	69.025	BR	200	0.01
8	10.391	23.153	25.997	CO	30	0.63

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
11.79-91.4	0.769	0.588	274	140
8.37-11.79	0.616	0.353	540	149
6.85-8.37	0.486	0.331	722	152
5.93-6.85	0.333	0.244	872	155
5.31-5.93	0.283	0.138	988	152
4.85-5.31	0.223	0.137	1115	154
4.49-4.85	0.184	0.086	1218	144
4.2-4.49	0.163	0.081	1240	150

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
BUSTER-TNT	BUSTER 2.10.0	refinement
SHARP		phasing
PDB_EXTRACT	3.11	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MIR / Resolution: 3.94→42.26 Å / Cor.coef. F_o:F_c: 0.9267 / Cor.coef. F_o:F_c free: 0.9112 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2752	411	4.72 %	RANDOM
R_work	0.2622	-	-	-
all	0.2622	9479	-	-
obs	0.2628	8706	92.23 %	-

Solvent computation

B_sol: 159.016 Å²

Displacement parameters

B_iso max: 285.13 Å² / B_iso mean: 220.6988 Å² / B_iso min: 134.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.762 Å²	0 Å²	0 Å²
2-	-	-23.219 Å²	0 Å²
3-	-	-	28.981 Å²

Refine analyze

Luzzati coordinate error obs: 1.31 Å

Refinement step

Cycle: LAST / Resolution: 3.94→42.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	4140	109	0	4249

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.003
X-RAY DIFFRACTION	c_angle_d	0.867
X-RAY DIFFRACTION	c_mcbond_it	30.189	15
X-RAY DIFFRACTION	c_mcangle_it	38.739	20

LS refinement shell

Resolution: 3.94→4.41 Å / Total num. of bins used: 9

	R_factor	Num. reflection	% reflection
R_free	0.2869	131	-
R_work	0.274	-	-
obs	-	2496	92.23 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.7708	-0.2893	-0.4552	0.8266	-0.1621	1.046	-0.003	-0.0056	0.0187	-0.0027	0.0083	0.0023	0.0006	-0.003	-0.0053	0.1415	0.0456	-0.0916	0.0853	-0.013	0.0382	-9.5088	-23.0948	26.6162
2	3.4947	-0.3385	1.6254	3.797	0.0074	3.8119	0.1073	0.2685	-0.1319	-0.3478	-0.0049	0.2327	0.4504	-0.5674	-0.1024	-0.1967	0.2184	-0.0403	-0.2211	-0.0222	-0.256	-8.9583	-29.945	23.8196

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ Z\|301 - Z\|301 }	Z	301
2	X-RAY DIFFRACTION	2	{ Z\|3 - Z\|210 }	Z	3 - 210

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