PDB-7qr1: SpCas9 bound to TRAC off-target2 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qr1

Title

SpCas9 bound to TRAC off-target2 DNA substrate

Components

(TRAC off-target2 ...) 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: 2.6 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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PDBx/mmCIF format	7qr1.cif.gz	826.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qr1_validation.pdf.gz	467.8 KB	Display	wwPDB validaton report
Full document	7qr1_full_validation.pdf.gz	483.6 KB	Display
Data in XML	7qr1_validation.xml.gz	51.7 KB	Display
Data in CIF	7qr1_validation.cif.gz	73.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qr/7qr1 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qr1	HTTPS FTP

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Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqrC 7qqsC 7qqtC 7qquC 7qqvC 7qqwC 7qqxC 7qqzC 7qr0C 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-target2 target strand

D: TRAC off-target2 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)	178.420, 66.795, 187.240
Angle α, β, γ (deg.)	90.000, 111.411, 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-target2 ... , 2 types, 2 molecules CD

#3: DNA chain	TRAC off-target2 target strand Mass: 8555.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	TRAC off-target2 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, 317 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.: 14 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 301 / 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 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: 2.6→46.14 Å / Num. obs: 63694 / % possible obs: 99.9 % / Redundancy: 6.8 % / B_iso Wilson estimate: 57.24 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.2 / Net I/σ(I): 9.4
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 7.1 % / R_merge(I) obs: 2.3 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6348 / CC_1/2: 0.318 / % possible all: 99.8

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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: 2.6→47.54 Å / SU ML: 0.4626 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2307	3178	4.99 %
R_work	0.206	60488	-
obs	0.2072	63666	99.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 68.46 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→47.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10856	2508	16	301	13681

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	13853
X-RAY DIFFRACTION	f_angle_d	0.5765	19196
X-RAY DIFFRACTION	f_chiral_restr	0.0381	2190
X-RAY DIFFRACTION	f_plane_restr	0.0031	2020
X-RAY DIFFRACTION	f_dihedral_angle_d	20.012	5615

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 (%)
2.6-2.64	0.4145	143	0.3785	2644	X-RAY DIFFRACTION	99.68
2.64-2.68	0.3883	132	0.3719	2591	X-RAY DIFFRACTION	99.85
2.68-2.72	0.3941	134	0.3679	2626	X-RAY DIFFRACTION	99.75
2.72-2.77	0.39	124	0.3393	2603	X-RAY DIFFRACTION	100
2.77-2.82	0.3435	149	0.33	2575	X-RAY DIFFRACTION	99.96
2.82-2.88	0.3589	144	0.3147	2636	X-RAY DIFFRACTION	99.93
2.88-2.93	0.3175	131	0.3048	2585	X-RAY DIFFRACTION	99.93
2.93-3	0.295	140	0.2919	2630	X-RAY DIFFRACTION	99.86
3-3.07	0.2851	136	0.2871	2643	X-RAY DIFFRACTION	100
3.07-3.14	0.3432	139	0.2851	2568	X-RAY DIFFRACTION	100
3.14-3.23	0.3167	132	0.2735	2619	X-RAY DIFFRACTION	99.93
3.23-3.32	0.2912	143	0.2475	2631	X-RAY DIFFRACTION	99.93
3.32-3.43	0.281	132	0.2342	2626	X-RAY DIFFRACTION	99.93
3.43-3.55	0.2596	146	0.2168	2623	X-RAY DIFFRACTION	99.96
3.55-3.7	0.2324	133	0.2024	2627	X-RAY DIFFRACTION	99.93
3.7-3.86	0.181	142	0.1852	2596	X-RAY DIFFRACTION	99.89
3.86-4.07	0.1797	139	0.171	2630	X-RAY DIFFRACTION	99.89
4.07-4.32	0.1714	140	0.1608	2657	X-RAY DIFFRACTION	99.96
4.32-4.66	0.1715	135	0.1543	2624	X-RAY DIFFRACTION	100
4.66-5.12	0.186	139	0.1451	2660	X-RAY DIFFRACTION	99.96
5.13-5.86	0.2316	137	0.1671	2651	X-RAY DIFFRACTION	99.79
5.87-7.38	0.1845	143	0.1786	2694	X-RAY DIFFRACTION	99.89
7.39-47.54	0.1696	145	0.1495	2749	X-RAY DIFFRACTION	99.69

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	0.0189025729817	-0.0118199218039	0.308525271606	-0.0263244522148	0.231647235569	0.887753646852	0.000172960304857	-0.112713361052	0.0162367110447	0.193239739477	0.0946901008755	0.136830704475	0.813598492335	-0.383959833397	0.0419266935895	0.478275283208	-0.0270552255225	0.0182306663535	0.289459221447	-0.0405555887261	0.362581082057	-6.43926808759	7.04964619962	59.8493777888
2	0.46321984397	0.139877415327	0.575901916872	0.265831866592	-0.114057023038	0.641702958098	0.120608707157	0.242354850551	0.12216457703	-0.121844190512	0.0580682862183	0.0409080958714	0.104018753254	0.200660790361	0.295549662099	0.476316690807	-0.00579411406924	-0.0381006417112	0.53604702501	0.00262899393544	0.337592969824	6.81956711125	1.39348629845	21.5474034294
3	0.0282858539956	-0.025399681472	0.0287116171599	0.0112110604323	-0.0131981856502	-0.00447936540261	0.0936440618122	0.0329623224695	0.174134605275	-0.502270343312	-0.0433865103082	0.17428983312	-0.773219104117	-0.0383626842521	0.000168453246344	0.820469107685	-0.175786408918	0.102227163991	0.934842160991	0.145982034324	0.938169597025	-39.8281185826	15.6901784298	33.5326819566
4	0.420135688954	0.305358596769	0.102942812799	0.216980433744	-0.271068076131	0.482893722507	0.0644485182556	0.282937250542	0.088138740075	0.0221780250657	-0.0749047403645	0.0292579551959	-0.0570641205653	0.096700629178	0.00392523649399	0.362095808681	-0.0503095540068	0.0217546820225	0.386417315562	-0.0124121146639	0.36137408551	5.73062892491	6.3554678751	37.0609731179
5	0.20330443267	0.0307364973358	0.0968307039072	0.179780581581	-0.202778049606	0.242741597766	-0.0360789097495	0.0285941245151	-0.096733319259	0.00720988295115	0.0722073549119	0.0238472811933	-0.0278847186805	-0.10875144063	4.90060646004E-5	0.595986748516	0.10305582858	0.0442384587323	0.437679113913	0.0188098217357	0.524351975251	23.5290174467	-3.7760185574	66.9600732241
6	0.372474336569	-0.219917892666	-0.120013923286	0.0394922193876	0.149505423229	1.00458378594	-0.00344510654519	0.0399811100262	0.0124670449299	0.0348264102247	0.000564916612171	0.0118082209226	-0.0267169582367	0.0939764541786	-3.52556496878E-6	0.335692322212	-0.0571474544635	1.69213934815E-5	0.286323015221	0.0144423836255	0.398804005778	11.2599967917	9.1865489262	56.5808496482
7	0.0572299841161	0.0960803628079	0.208782788479	0.0821146336736	-0.0471842689126	0.301414503822	-0.0205637483106	0.0474545463234	0.0426205798245	0.0334098043413	0.0240016385299	0.046030584647	-0.0264727193254	-0.106738864191	-5.64286324834E-6	0.34491877047	0.00106662376717	0.0332445712202	0.305018074601	-0.0212130274485	0.394455049851	-14.5470254761	13.141339653	66.3396462016
8	0.193311328645	-0.0199050904258	0.102029956546	0.636107037263	0.0720881852634	0.214387209874	0.00572400434258	-0.117129241743	0.0443754182636	-0.15401656729	0.0164537398677	-0.015571604752	0.0406764062474	-0.05878934767	7.19972801492E-6	0.542032284525	0.0134196938652	-0.00598811568564	0.47692473162	0.00922801641127	0.58138392884	-1.75948934149	-18.7679804456	68.8091122202
9	0.83818393134	0.193269140011	-0.185104732458	0.132978109673	-0.0644378285098	0.556571368592	-0.0789106108932	0.210129684029	-0.0904230997449	-0.0347240617749	0.0698384487324	-0.0046570472634	0.165155725855	-0.118423570493	-5.32951733719E-6	0.363981425476	-0.0934996928788	0.0198766170976	0.316552140726	-0.0163406221197	0.350187597898	-29.725763302	-11.8889198638	42.9325068079
10	0.00299133797395	0.00794394833383	-0.000207919289611	0.00745388498107	-0.00833733207875	-0.00121745458082	0.00289649885111	0.0899927734027	-0.0565151926557	0.262473395294	-0.00822153173746	0.00232982055087	-0.000292066810394	-0.185353217961	5.26789384158E-6	0.833935503	-0.302079348176	-0.0417580369459	1.23484799217	-0.347518842209	0.865677034104	-15.958417311	-21.8663049798	19.1674065641
11	-0.000171154393445	0.00345476701546	-0.00791197624418	0.0044250154054	-0.0144592896357	0.021024838759	0.0881659465015	-0.10264121054	0.0262437584968	0.0372293798452	-0.050484458536	0.098560493993	0.123658704623	0.058929773925	-3.6901843687E-5	0.404229702614	0.00479137619323	-0.00810254855704	0.505808453535	-0.0770226906129	0.312624531574	-2.76198657685	-9.45627575512	31.0539328294
12	0.000236728456623	0.123509903049	0.138128144509	-0.0730279074896	0.0519845387804	0.0251386145131	0.0772629950352	0.161760351146	0.23853380551	0.0428274127938	0.222368286651	0.11689187801	0.153384552621	-0.433302101384	-5.49931904231E-5	0.457716872448	-0.0570972643963	0.0497628670927	0.4341860552	0.00982080403605	0.410527905899	-7.45174774621	5.26467178167	64.9803916119
13	0.857536891323	0.470716966871	0.174744038328	0.799020575282	-0.173777243587	0.185742172619	0.511425690123	0.0605904155455	-0.902713211357	0.342234263834	0.257438309363	-0.355736668009	0.179442851898	0.3383754623	0.14522495987	0.412281603694	-0.0457519036951	0.00786463016153	0.455997245295	-0.280244730975	0.407071317243	-11.6949508657	-14.5825402585	23.5468164209

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 69 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 70 through 82 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 3 through 207 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 208 through 286 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 287 through 639 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 640 through 791 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 792 through 909 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 910 through 1367 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid -7 through -3 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid -2 through 2 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 3 through 20 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid -2 through 7 )

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