PDB-7os0: Structure of the Rhodobacter capsulatus Cas13a-crRNA binary complex

ID or keywords:

Entry

Database: PDB / ID: 7os0

Title

Structure of the Rhodobacter capsulatus Cas13a-crRNA binary complex

Components

Cas13a
crRNA

Keywords

RNA BINDING PROTEIN / RNA dependent RNase / CRISPR-associated gene / endonuclease

Function / homology

: / nuclease activity / defense response to virus / RNA binding / BETA-MERCAPTOETHANOL / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a

Function and homology information

Biological species

Rhodobacter capsulatus SB 1003 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Kick, L.M. / Schneider, S.

Funding support

Germany, 4items

Organization	Grant number	Country
German Research Foundation (DFG)	SPP 2141	Germany
German Research Foundation (DFG)	SFB1309	Germany
German Research Foundation (DFG)	SCHN 1273-6	Germany
German Research Foundation (DFG)	CIPSM, EXC114	Germany

Citation

Journal: Commun Biol / Year: 2022
Title: Structure and mechanism of the RNA dependent RNase Cas13a from Rhodobacter capsulatus.
Authors: Kick, L.M. / von Wrisberg, M.K. / Runtsch, L.S. / Schneider, S.

History

Deposition	Jun 7, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 9, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7os0.cif.gz	1000.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7os0.ent.gz	827.1 KB	Display	PDB format
PDBx/mmJSON format	7os0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/7os0 ftp://data.pdbj.org/pub/pdb/validation_reports/os/7os0	HTTPS FTP

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Related structure data

Similar structure data	7os0-2 7kf3-d 2j55-d 7vym-d 7c4n-1 6vzg-d 4rs0-1 9789 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&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 (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance 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) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase 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) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme 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 (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
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)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
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)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#252 - Dec 2020
Hepatitis C Virus Protease/Helicase
similarity (1)
#9 - Sep 2000
Lysozyme
similarity (1)

Deposited unit

A: Cas13a

C: Cas13a

D: crRNA

F: crRNA

hetero molecules

326 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cas13a

F: crRNA

hetero molecules

defined by author&software
Evidence: gel filtration
163 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cas13a

D: crRNA

hetero molecules

defined by author&software
Evidence: gel filtration
163 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.387, 91.082, 136.509
Angle α, β, γ (deg.)	89.990, 103.690, 97.650
Int Tables number	1
Space group name H-M	P1

#1: Protein	Cas13a Mass: 145524.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria) Gene: RCAP_rcc02005 / Production host: Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AUW0
#2: RNA chain	crRNA Mass: 17175.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆OS
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM MES pH 6.0, 200 mM NaCl and 20 % (w/v) PEG6000

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 7, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 2.2→47.12 Å / Num. obs: 141242 / % possible obs: 97.6 % / Redundancy: 3.6 % / B_iso Wilson estimate: 41.8 Å² / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.085 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2.2→2.3 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.913 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 14010 / CC_1/2: 0.726 / CC star: 0.917 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
XDS	VERSION Jan 26, 2018	data reduction
XSCALE		data scaling
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→47.12 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.931 / SU B: 16.16 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2557	7063	5 %	RANDOM
R_work	0.2183	-	-	-
obs	0.2202	134180	97.75 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso max: 266.64 Å² / B_iso mean: 91.005 Å² / B_iso min: 26.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.65 Å²	-0.77 Å²	2.89 Å²
2-	-	-0.87 Å²	-0.07 Å²
3-	-	-	-0.86 Å²

Refinement step

Cycle: final / Resolution: 2.2→47.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17734	1986	56	630	20406
B_iso mean	-	-	69.1	51.61	-
Num. residues	-	-	-	-	2349

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.017	20459
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.019	18587
X-RAY DIFFRACTION	r_angle_refined_deg	1.014	1.797	27982
X-RAY DIFFRACTION	r_angle_other_deg	1.013	2.661	42754
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.997	5	2259
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.52	20.188	1064
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.697	15	3197
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.46	15	202
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	3029
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	21685
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4899
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.257 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.405	514	-
R_work	0.369	9760	-
all	-	10274	-
obs	-	-	96.36 %

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	0.4146	-0.3814	0.3896	4.2885	0.2337	0.7484	-0.0132	-0.0528	-0.0797	0.1051	0.1599	0.2137	0.1553	-0.0085	-0.1467	0.3193	0.085	-0.1063	0.0443	-0.0627	0.268	-9.494	43.417	100.742
2	1.0108	-3.7136	1.18	14.0673	-4.1217	2.456	-0.0268	0.1528	0.2891	0.2999	-0.5577	-1.2645	-0.4069	0.267	0.5845	0.493	-0.0422	-0.1246	0.2766	-0.0265	0.4678	-3.057	81.096	85.642
3	1.6535	3.0006	0.0473	12.1111	8.4371	10.5337	0.5845	-0.0909	0.1478	0.1099	-0.4052	0.0517	-1.1418	-0.518	-0.1793	0.8018	0.1135	-0.0246	0.7266	-0.0321	0.8922	8.906	77.044	77.873
4	6.4725	3.2461	-1.6148	3.1483	0.5833	1.6868	0.0277	-0.7731	-1.0493	0.2804	-0.3599	-0.4653	0.3051	0.2279	0.3322	0.7987	0.1153	-0.0429	0.2816	-0.0577	0.6072	-3.572	55.465	72.247
5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.2444	0	0	0.2444	0	0.2444	0	0	0
6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.2444	0	0	0.2444	0	0.2444	0	0	0
7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.2444	0	0	0.2444	0	0.2444	0	0	0
8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.2444	0	0	0.2444	0	0.2444	0	0	0
9	1.6526	-0.283	-0.2558	3.5582	-1.3663	2.5124	0.1833	0.1337	0.2506	-0.4444	0.0122	-0.1662	-0.1563	0.073	-0.1955	0.426	0.0847	-0.0455	0.0872	-0.1403	0.4026	31.233	140.121	24.718
10	0.5657	0.2757	-0.1942	2.6622	0.3125	0.3906	-0.0173	-0.0145	0.0305	0.1947	0.0329	0.1842	-0.0301	-0.0103	-0.0156	0.3646	0.1471	-0.1167	0.077	-0.1038	0.2295	8.561	117.644	42.313
11	2.4848	1.4623	-2.1904	1.7026	-1.7795	3.3164	-0.0066	-0.3149	-0.1555	0.1235	-0.085	0.0425	-0.0656	0.3393	0.0916	0.374	0.148	-0.1071	0.1299	-0.0775	0.3713	21.66	80.418	31.964
12	1.0311	0.4272	-0.6556	1.6796	-0.1174	0.8285	-0.0491	0.029	0.0266	-0.0486	0.0722	-0.0763	-0.0181	0.0151	-0.0231	0.3693	0.1537	-0.1599	0.0924	-0.1347	0.3003	27.825	99.575	22.037
13	0.7939	0.6157	-0.6209	2.3047	-0.6387	1.3889	-0.2639	0.1583	-0.2965	-0.4678	0.0794	-0.1743	0.2854	-0.0908	0.1845	0.4936	0.1038	-0.0875	0.1405	-0.2378	0.4414	1.789	91.993	6.401
14	0.5912	0.2682	0.075	1.2418	0.6989	3.2616	-0.0032	0.0714	0.0123	-0.0075	0.023	0.1961	-0.0333	-0.1027	-0.0198	0.2839	0.1282	-0.1219	0.0797	-0.095	0.2976	0.609	109.091	24.16
15	0.7283	-0.1384	0.5401	1.7106	-0.1713	1.8873	0.0638	0.076	-0.0658	-0.1505	0.0233	0.0992	0.2912	-0.0181	-0.0871	0.4687	0.0856	-0.1163	0.0524	-0.1092	0.4089	-9.445	38.025	95.062
16	0.4967	0.0785	0.3864	1.516	0.5752	1.484	-0.003	-0.0198	-0.0388	-0.1422	0.0995	-0.0606	-0.2165	-0.0213	-0.0965	0.4242	0.1289	-0.0705	0.0821	-0.1257	0.3653	-7.177	83.413	91.469
17	0.4522	-0.0397	-0.4623	1.5634	0.6427	1.9345	0.145	-0.0584	0.1296	-0.1955	0.2554	-0.4824	-0.3768	0.4461	-0.4003	0.4319	0.0602	-0.0527	0.1961	-0.2531	0.545	13.662	71.609	90.633
18	0.21	-0.4518	-0.3319	1.0142	0.732	0.5332	-0.1153	-0.0176	0.0065	0.1845	0.1349	-0.0514	0.1729	0.0768	-0.0195	0.4743	0.0087	-0.0794	0.2999	-0.1118	0.4246	6.809	53.489	97.554

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	D	12 - 36
2	X-RAY DIFFRACTION	2	D	37 - 41
3	X-RAY DIFFRACTION	3	D	42 - 46
4	X-RAY DIFFRACTION	4	D	47 - 54
5	X-RAY DIFFRACTION	5	F - f	7 - 11
6	X-RAY DIFFRACTION	6	F - f	12 - 36
7	X-RAY DIFFRACTION	7	F - f	37 - 41
8	X-RAY DIFFRACTION	8	F - f	42 - 54
9	X-RAY DIFFRACTION	9	A	1 - 168
10	X-RAY DIFFRACTION	10	A	169 - 484
11	X-RAY DIFFRACTION	11	A	485 - 564
12	X-RAY DIFFRACTION	12	A	565 - 849
13	X-RAY DIFFRACTION	13	A	850 - 964
14	X-RAY DIFFRACTION	14	A	965 - 1166
15	X-RAY DIFFRACTION	15	C	1 - 360
16	X-RAY DIFFRACTION	16	C	361 - 887
17	X-RAY DIFFRACTION	17	C	888 - 1166
18	X-RAY DIFFRACTION	18	D	7 - 11

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+
Jul 12, 2017. Major update of PDB

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Yorodumi