PDB-7qr0: SpCas9 bound to TRAC off-target1 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qr0

Title

SpCas9 bound to TRAC off-target1 DNA substrate

Components

(TRAC off-target1 ...) x 2
CRISPR-associated endonuclease Cas9/Csn1
TRAC sgRNA

Keywords

HYDROLASE / crispr / cas9 / off-target / ternary complex

Function / homology

Function and homology information

maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function

Biological species

Streptococcus pyogenes (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Pacesa, M. / Jinek, M.

Funding support

Switzerland, 1items

Citation

Journal: Cell / Year: 2022
Title: Structural basis for Cas9 off-target activity.
Authors: Pacesa, M. / Lin, C.H. / Clery, A. / Saha, A. / Arantes, P.R. / Bargsten, K. / Irby, M.J. / Allain, F.H. / Palermo, G. / Cameron, P. / Donohoue, P.D. / Jinek, M.

History

Deposition	Jan 10, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 26, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7qr0_validation.pdf.gz	471 KB	Display	wwPDB validaton report
Full document	7qr0_full_validation.pdf.gz	486.6 KB	Display
Data in XML	7qr0_validation.xml.gz	55.4 KB	Display
Data in CIF	7qr0_validation.cif.gz	81.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qr/7qr0 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qr0	HTTPS FTP

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Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqrC 7qqsC 7qqtC 7qquC 7qqvC 7qqwC 7qqxC 7qqzC 7qr1C 7qr5C 7qr7C 7qr8C 7zo1C 5fq5S 7ox8 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: TRAC sgRNA

B: CRISPR-associated endonuclease Cas9/Csn1

C: TRAC off-target1 target strand

D: TRAC off-target1 non-target strand

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	177.547, 67.421, 187.247
Angle α, β, γ (deg.)	90.000, 111.488, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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TRAC off-target1 ... , 2 types, 2 molecules CD

#3: DNA chain	TRAC off-target1 target strand Mass: 8589.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	TRAC off-target1 non-target strand Mass: 3692.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain / Protein , 2 types, 2 molecules AB

#1: RNA chain	TRAC sgRNA Mass: 27133.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein	CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9 Mass: 158588.781 Da / Num. of mol.: 1 / Mutation: D10A, H840A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

#1: RNA chain

TRAC sgRNA

Mass: 27133.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#2: Protein

CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9

Mass: 158588.781 Da / Num. of mol.: 1 / Mutation: D10A, H840A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pyogenes (bacteria) / Gene: cas9, csn1, SPy_1046 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 677 molecules

#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.64 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 20, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→46.13 Å / Num. obs: 92030 / % possible obs: 99.9 % / Redundancy: 6.8 % / B_iso Wilson estimate: 49.26 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.14 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 6.6 % / R_merge(I) obs: 1.91 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9144 / CC_1/2: 0.339 / % possible all: 100

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Processing

Software

Name	Version	Classification
Coot		model building
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FQ5

5fq5

Resolution: 2.3→47.71 Å / SU ML: 0.3307 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2238	4601	5 %
R_work	0.1939	87397	-
obs	0.1954	91998	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 66.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→47.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10891	2500	19	658	14068

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0018	13881
X-RAY DIFFRACTION	f_angle_d	0.4504	19234
X-RAY DIFFRACTION	f_chiral_restr	0.0347	2194
X-RAY DIFFRACTION	f_plane_restr	0.0027	2027
X-RAY DIFFRACTION	f_dihedral_angle_d	17.859	5627

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.33	0.3218	155	0.3329	2949	X-RAY DIFFRACTION	99.81
2.33-2.35	0.3655	151	0.3218	2857	X-RAY DIFFRACTION	99.97
2.35-2.38	0.3732	149	0.3282	2880	X-RAY DIFFRACTION	100
2.38-2.41	0.3429	156	0.3164	2917	X-RAY DIFFRACTION	99.87
2.41-2.44	0.3564	155	0.3056	2864	X-RAY DIFFRACTION	99.93
2.44-2.48	0.3361	152	0.3023	2872	X-RAY DIFFRACTION	99.97
2.48-2.51	0.3403	147	0.2931	2914	X-RAY DIFFRACTION	99.9
2.51-2.55	0.3373	152	0.2876	2868	X-RAY DIFFRACTION	99.97
2.55-2.59	0.3316	157	0.2817	2925	X-RAY DIFFRACTION	100
2.59-2.63	0.3186	155	0.2669	2904	X-RAY DIFFRACTION	99.97
2.63-2.68	0.2836	152	0.256	2874	X-RAY DIFFRACTION	99.97
2.68-2.73	0.3172	147	0.2599	2898	X-RAY DIFFRACTION	99.97
2.73-2.78	0.2821	152	0.2591	2921	X-RAY DIFFRACTION	100
2.78-2.84	0.3031	157	0.2525	2865	X-RAY DIFFRACTION	99.97
2.84-2.9	0.309	152	0.2477	2928	X-RAY DIFFRACTION	99.97
2.9-2.97	0.2834	151	0.2417	2928	X-RAY DIFFRACTION	100
2.97-3.04	0.2704	152	0.2413	2888	X-RAY DIFFRACTION	100
3.04-3.12	0.2829	152	0.2253	2894	X-RAY DIFFRACTION	99.97
3.12-3.21	0.2581	158	0.2148	2927	X-RAY DIFFRACTION	100
3.21-3.32	0.2297	153	0.2003	2898	X-RAY DIFFRACTION	99.97
3.32-3.44	0.2481	147	0.1896	2918	X-RAY DIFFRACTION	99.84
3.44-3.57	0.1963	156	0.1854	2891	X-RAY DIFFRACTION	99.87
3.57-3.74	0.201	155	0.1787	2939	X-RAY DIFFRACTION	99.81
3.74-3.93	0.171	150	0.1581	2912	X-RAY DIFFRACTION	99.97
3.93-4.18	0.1714	157	0.1485	2921	X-RAY DIFFRACTION	100
4.18-4.5	0.1482	153	0.1415	2966	X-RAY DIFFRACTION	100
4.5-4.95	0.1618	158	0.1383	2918	X-RAY DIFFRACTION	100
4.95-5.67	0.2048	155	0.1486	2950	X-RAY DIFFRACTION	99.84
5.67-7.14	0.1962	155	0.1771	2959	X-RAY DIFFRACTION	99.74
7.14-47.71	0.1823	160	0.1616	3052	X-RAY DIFFRACTION	99.35

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	0.167988425695	0.324653967599	0.427750334657	1.54121577558	2.38107036259	3.711508009	0.137155629058	0.0292334567976	0.341366846857	0.408482682713	0.0353524512968	0.424138027706	0.468728975974	-0.433847194769	-0.203889917856	0.607352935901	-0.102144612946	0.047026740911	0.614666133247	0.0233309532006	0.539454855823	-15.1368427492	3.34505165181	77.8074041586
2	4.56934832613	-0.690431763821	-0.945873270085	5.35718685187	0.611284442524	4.31936122713	0.356294732804	0.532203576158	-1.01774552696	-0.179596598912	0.206738418047	-0.322934235782	0.910538129243	0.385042112516	-0.401124435912	0.522636503836	-0.0492035326573	-0.0253086928648	0.431743571414	-0.212169163784	0.660180947315	-11.5446072271	-14.4796820277	24.0948454575
3	1.0234840735	-1.29743610367	-0.269070423742	5.27825916636	2.94821048652	6.66391735621	-0.125635377757	0.0567585575821	-0.260071818301	0.0654983872673	-0.298341140003	0.745680702599	0.259194844978	-0.707016331383	0.457468695874	0.572958069705	-0.138532239047	0.0482865808833	0.599698974406	-0.10398679391	0.544582346574	-10.7376860041	5.88727287636	71.5959496155
4	1.43363681029	-0.168805535227	-0.188833660726	0.849260206303	0.670060722603	1.5672361047	0.0487882021066	0.0470866834314	0.00681083729881	0.15946089735	0.129283789746	-0.0659218235808	0.370153864591	0.340691394701	-0.0508190483117	0.429295319208	0.0350228969947	0.00204068688144	0.428220426813	-0.00811156603324	0.395919147177	8.38167974465	3.32949447782	31.5891259903
5	0.110265200068	0.00593082742704	0.545464189126	0.224775088914	0.159170552864	2.98813037808	0.424127300082	0.582577948246	-0.0336271733631	-0.996896311857	0.0724077392908	0.521744253622	0.504673833323	0.160265674972	-0.307316556523	1.34571767446	0.235308353524	-0.151386435976	1.54277762237	-0.206861291717	0.845781749004	22.5471208935	-18.1040571163	1.72837960777
6	0.955256346913	0.167752311266	0.517771955966	0.711777533665	-0.0855140213931	1.26346768902	0.0084698765502	0.210884192745	0.148093109853	-0.0512143498624	0.018765955993	0.0799224421032	0.00446145872389	0.116478737165	-0.0647684600641	0.339377949453	-0.0412642188658	-0.02012021451	0.362810853249	0.00711362295667	0.35359605598	-3.22743765906	9.74763923921	29.4045848351
7	0.0334281812154	0.240149090021	-0.00145504391979	1.90942539107	-0.0661555049211	0.0464118142334	-0.0032365451713	0.0698761775187	0.489185073182	-0.760756239351	-0.0126606672715	-0.734868261828	-1.84224722399	1.15190625844	-0.140582310643	1.59512677514	-0.382787927761	0.379124876316	1.13034531567	0.222604209702	1.46757570476	-37.4651907536	19.9193227883	29.3069209986
8	3.56959764002	-0.856707360513	0.324225242879	4.20750919324	0.740473179668	5.34496627334	0.177575727667	-0.364137188297	0.23379027349	-0.517377224536	-0.00425039663593	-0.630623592503	-1.55149260959	0.650338398644	-0.120912987886	0.796896729495	-0.197509038963	0.120119709561	1.00635864326	-0.0293662993014	0.8761764187	-41.1791017652	13.6300752665	37.7704504959
9	0.982942448887	0.362266993664	0.0154233422499	0.367569930194	-0.195664085322	0.899950103582	0.0937346625676	0.107135451786	0.0502130069701	0.0604030035664	-0.0656772944736	-0.013975406575	-0.0210446621721	0.249001210084	-0.0269865860577	0.354732221235	-0.0390324470191	0.0108386395464	0.367331449398	-0.0443647821603	0.356369502795	5.34792318789	6.60824541338	37.1133095924
10	2.29503997182	-0.811426067118	0.391942563243	1.98009244686	-0.82022336909	3.25805576432	0.137191845875	0.347677212267	-0.333407746946	-0.0758969398116	-0.266526917835	0.582530543006	-0.822467119558	-1.20777026401	0.0293183384849	0.807922050794	0.215992094566	-0.0430179211282	0.804319028787	-0.104847783349	0.726152814682	23.2017744886	-3.76288921423	66.4596382826
11	0.458868435939	-0.143210194571	-0.093613013399	0.236519314594	0.149266357064	1.78766550961	0.00580068937959	0.0030717862431	0.00402154966806	0.095748026306	0.0744553018571	-0.0589995924694	0.0201537504959	0.302740083675	-0.0668967033919	0.36393246053	-0.0236511148728	-0.0368796030166	0.342679102595	-0.00371044426678	0.423780748605	10.2574482166	11.0780768472	58.3560098293
12	0.232999631837	0.0515359595855	0.172179389025	0.29745803272	0.0500627576717	0.8836008119	-0.0142903581928	-0.0694464563877	-0.112979154241	0.110950067888	0.0831384193777	-0.0356599465953	0.196729564864	0.0303350228145	-0.0428076402227	0.519564095152	0.0184244700968	0.0262009290135	0.495920206679	-0.00544048680888	0.540608607927	-10.7539250799	-6.25280589041	66.2980325549
13	1.31118600749	0.153987307168	-0.369530553639	0.461862960344	-0.0192410698684	1.40302265957	-0.100516327508	0.0760268680113	-0.208398325436	0.0428897268335	0.0828661331128	0.0411532205008	0.437964550001	-0.257318759148	0.00795028478438	0.436216341237	-0.112858951188	0.00507167711972	0.315752462713	-0.0152681103151	0.436731860467	-29.7481324458	-11.7408883126	42.9360136477
14	0.85235107423	0.80932557551	0.502098081608	1.28752184315	0.429711427729	1.42904364561	0.177032943426	0.167803866318	-0.488120081476	0.145129000366	-0.0630502608575	0.0546510926943	0.0472813817101	-0.786629591782	-0.054985931274	1.11451001057	-0.337858301576	-0.0494878262208	1.56922587338	-0.5075125216	1.01066916459	-15.7910946824	-21.7923043395	19.2358468947
15	2.53159900933	1.47355426236	-0.129587643193	2.60377395445	-0.548452784755	0.852412282639	0.284860201747	-0.0421232140308	-0.400192405252	-0.0313864338794	-0.380259327366	0.225266212102	0.483964421642	0.271141273245	0.0079455005261	0.492128685982	0.0253157614716	-0.0424049616117	0.391037955175	-0.0402931836957	0.429652961777	-2.69251639038	-9.18189341959	31.1100943264
16	3.13446794975	-1.64032897502	-0.789869265834	3.65735086657	2.4017307144	4.0163806119	0.0708366055384	0.347888481415	0.140383971894	0.719153735147	0.41840163747	-0.360509233784	0.914036931716	-0.204262309342	-0.367348392972	0.562366104186	-0.102487455524	-0.0378340279318	0.449270371003	-0.00137221738919	0.420715304301	5.91301704801	4.06533989628	48.7869858683
17	0.523893052573	-0.496924660829	-0.83760655824	2.40860976881	-0.513558484718	2.23844283233	0.132475073413	0.11072368955	0.362439420755	0.44889462398	0.11287570674	0.54161868818	0.0677774761192	-0.314451186071	-0.231319654493	0.503092380643	-0.0611377342593	0.112741506708	0.453926906161	0.0309673466117	0.49816600854	-8.56651027423	10.1821398395	60.3583153251

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 13 through 20 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid -3 through 7 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1 through 10 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 11 through 30 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 31 through 40 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 41 through 70 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 71 through 75 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 76 through 82 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 207 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 208 through 284 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 285 through 678 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 679 through 909 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 910 through 1367 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -7 through -3 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid -2 through 2 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 3 through 7 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 8 through 12 )

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