PDB-7qr7: SpCas9 bound to AAVS1 off-target2 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qr7

Title

SpCas9 bound to AAVS1 off-target2 DNA substrate

Components

(AAVS1 off-target2 ...) x 2
AAVS1 sgRNA
CRISPR-associated endonuclease Cas9/Csn1

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: 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	7qr7_validation.pdf.gz	468.8 KB	Display	wwPDB validaton report
Full document	7qr7_full_validation.pdf.gz	483 KB	Display
Data in XML	7qr7_validation.xml.gz	50.3 KB	Display
Data in CIF	7qr7_validation.cif.gz	70.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qr/7qr7 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qr7	HTTPS FTP

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Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqrC 7qqsC 7qqtC 7qquC 7qqvC 7qqwC 7qqxC 7qqzC 7qr0C 7qr1C 7qr5C 7qr8C 7zo1C 5fq5S 7ox9 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: AAVS1 sgRNA

B: CRISPR-associated endonuclease Cas9/Csn1

C: AAVS1 off-target2 target strand

D: AAVS1 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)	176.753, 67.129, 186.633
Angle α, β, γ (deg.)	90.000, 110.996, 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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AAVS1 off-target2 ... , 2 types, 2 molecules CD

#3: DNA chain	AAVS1 off-target2 target strand Mass: 8455.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	AAVS1 off-target2 non-target strand Mass: 3739.435 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	AAVS1 sgRNA Mass: 27290.303 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: D10, 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

AAVS1 sgRNA

Mass: 27290.303 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: D10, 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, 154 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.: 13 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 139 / 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: Feb 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→47.66 Å / Num. obs: 41411 / % possible obs: 99.8 % / Redundancy: 6.8 % / B_iso Wilson estimate: 78.55 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.22 / Net I/σ(I): 9
Reflection shell	Resolution: 3→3.11 Å / Redundancy: 6.8 % / R_merge(I) obs: 2.35 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4115 / CC_1/2: 0.332 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874+SVN	refinement
Coot		model building
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FQ5

5fq5

Resolution: 3→47.66 Å / SU ML: 0.4642 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2451	2065	4.99 %
R_work	0.2161	39302	-
obs	0.2176	41367	99.79 %

Solvent computation

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

Displacement parameters

B_iso mean: 98 Å²

Refinement step

Cycle: LAST / Resolution: 3→47.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10839	2529	15	139	13522

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13859
X-RAY DIFFRACTION	f_angle_d	0.5639	19213
X-RAY DIFFRACTION	f_chiral_restr	0.0382	2195
X-RAY DIFFRACTION	f_plane_restr	0.003	2017
X-RAY DIFFRACTION	f_dihedral_angle_d	19.0185	5616

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 (%)
3-3.07	0.3693	132	0.3702	2628	X-RAY DIFFRACTION	99.78
3.07-3.15	0.3917	138	0.3574	2575	X-RAY DIFFRACTION	99.82
3.15-3.23	0.3816	134	0.3329	2596	X-RAY DIFFRACTION	99.93
3.23-3.33	0.3355	137	0.3016	2604	X-RAY DIFFRACTION	99.82
3.33-3.43	0.3674	141	0.2909	2599	X-RAY DIFFRACTION	99.78
3.43-3.56	0.2724	137	0.2649	2575	X-RAY DIFFRACTION	99.6
3.56-3.7	0.299	131	0.2587	2602	X-RAY DIFFRACTION	99.6
3.7-3.87	0.2499	140	0.229	2604	X-RAY DIFFRACTION	99.82
3.87-4.07	0.2223	138	0.2161	2589	X-RAY DIFFRACTION	99.49
4.07-4.33	0.222	137	0.1919	2648	X-RAY DIFFRACTION	99.89
4.33-4.66	0.2221	139	0.177	2602	X-RAY DIFFRACTION	99.89
4.66-5.13	0.1951	138	0.1732	2643	X-RAY DIFFRACTION	100
5.13-5.87	0.2381	138	0.184	2641	X-RAY DIFFRACTION	99.93
5.87-7.39	0.2387	142	0.2007	2668	X-RAY DIFFRACTION	99.86
7.39-47.66	0.1878	143	0.1727	2728	X-RAY DIFFRACTION	99.72

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	1.25733216312	-1.33163206385	-0.937468567561	6.6146219899	1.05241360456	5.9597107553	-0.77731131384	0.314955000377	-0.566309149957	0.0473117044606	0.452082845282	-0.317231162325	0.641959088186	-1.32813986299	0.0820722930825	0.80931555339	-0.0767466944851	0.0642980901125	0.905079000023	-0.216883778355	0.877282984743	-13.6210214032	5.88977957356	74.7975854424
2	1.82316428387	-0.799791109991	-0.359928238058	0.0671055828178	-0.123795825571	2.35868154983	0.25636896156	-0.0552577834148	0.657100020412	0.37412145161	0.203784728001	-0.102486039309	0.533990534305	-0.0114745226399	-0.600167688539	0.650264987861	-0.17995564204	0.0742160486779	0.554137009944	-0.0309908406276	0.695774325552	5.71587579715	3.19742989522	37.1837048326
3	0.446818157636	0.426074813791	0.99287834844	0.65066814154	1.15561976591	2.39637329096	0.572844726608	0.460845182785	-0.325469364322	-1.20562358678	-0.320171558063	0.582334473889	0.919764592109	0.128898051902	-0.292593812327	1.46398335631	0.264978583758	-0.215473953639	2.11596402338	-0.163723740738	1.14141695563	22.0381151306	-16.4420420035	1.7190273226
4	1.79667861906	0.238633845426	0.264110645475	-0.127168354551	0.0360224756656	1.53606122149	-0.0929212775652	0.253355478942	-0.00125757660177	-0.0272480593731	-0.00694227672873	0.121923033922	-0.034013509637	0.0430601177602	0.0660204233634	0.581786743495	-0.102262884144	-0.0551731829989	0.44671461218	0.0157864573517	0.578813785291	1.7068484745	7.25420030618	28.2371933833
5	0.549504537551	-0.0360715692663	-0.741940143889	-0.000958298599564	0.0283422324235	1.26272193403	1.14793517073	0.422170655992	2.45301099904	-0.173211911314	-0.0398637400042	0.851204022861	-2.46278617161	0.620954375926	-0.278822049945	1.17986296117	0.226173163321	0.295474511598	0.927333408041	0.211684450126	1.78579308128	-39.3469048859	13.0657413174	29.9716677586
6	3.37439945528	0.184149527537	-1.52092803107	3.29581043598	-2.01406051823	3.90468891292	0.318055235312	-0.357317297639	0.612632110011	-0.409472399867	-0.117662878447	-0.000604431823057	-0.957612079117	1.18761074255	-0.330963682563	1.43274723584	-0.215193793062	0.0727528387882	1.65085878482	-0.0986467378653	1.24990779051	-38.5290858717	15.2401706573	36.2578343252
7	2.09005493719	0.595738845075	-0.0775822255756	0.4164257868	-0.306369954611	1.35866353377	0.165464013333	0.0367975108491	0.122533282894	0.13033378004	-0.14509517963	0.010086107737	-0.0420534009323	0.379287156638	-0.0066302442112	0.501551815343	-0.016069858237	-0.011363001865	0.322863781428	-0.0473884339987	0.51657206761	6.39050649805	5.89191041756	37.1653366871
8	1.46068725511	0.235313196763	1.09466662541	0.342073436997	-1.08310443774	2.35985984952	0.0774531371745	-0.0832258501284	-0.0841149014568	0.18249523163	-0.0270777173375	0.0597696238985	0.112042126756	-0.039960686962	-0.0344720346445	0.737023299621	0.141388842129	0.0175558576637	0.812556119163	0.00237160898144	0.690221271238	24.8750780046	-8.47191712855	47.5317945451
9	0.732027281896	0.100606609015	-0.330179366125	0.513629672778	-0.41504301449	2.6787782941	0.0015796349207	-0.115617463504	0.105352583877	0.253562728426	0.0870118169613	-0.086082402541	-0.505783801339	0.00574107346727	-0.0728390113248	0.639797267446	-0.0167211446713	-0.0258747249485	0.443487942349	-0.037172842415	0.669472528394	0.890595846126	19.7297800963	69.315996731
10	1.42253346756	-0.236661262884	0.641598448269	1.01180156348	-0.309685772024	1.90226014048	0.297358080105	-0.177576269049	-0.287165127618	0.0835414548203	-0.0762878399321	-0.290112108152	0.732273079162	0.474538081023	-0.174713839666	0.847952535971	0.0318681538627	-0.04943809383	0.795575433322	-0.117908799726	0.798695000506	-7.51608995515	-15.3502533681	62.749738849
11	1.37307442816	0.15945845982	-0.354197874968	0.710668473331	-0.155823335096	1.60164215055	-0.0778343790388	-0.0296868591839	-0.113644509508	0.061460938499	0.117885673782	0.0598814554656	0.370946409876	-0.286510893585	-0.0331534042828	0.594419506113	-0.146101292097	-0.00115674489709	0.563716358305	-0.0185851119105	0.639315372081	-27.9406895912	-12.4479726387	44.5733634867
12	2.24925204271	1.16691837334	1.62162220585	0.666239271672	0.81538410322	1.2801882677	0.550612705548	0.724063161641	-0.242862579838	0.330484823342	0.241844721906	0.78074277688	0.372539714506	-1.03925364774	-0.484401948559	1.34663010328	-0.517299893006	-0.0509944383442	2.01393766998	-0.416829070098	1.39689922386	-15.7450471479	-20.8630044648	18.5281357279
13	1.9926626151	1.84884897895	-0.0492221163889	2.70027868656	-0.157085771531	0.0349135662008	0.270316733738	-0.149131549432	-0.196005833479	0.451351221168	-0.180960923167	0.154545313278	0.807670667229	0.185876351834	0.11635570379	1.07695220581	0.0466018099032	-0.194174982979	0.717948562958	-0.147105841491	1.02237161941	-2.2979643177	-10.133280688	30.8162342967
14	3.33440570389	0.388574755696	-2.28664625263	0.574780035949	-0.530428255966	1.89955974846	0.41087165949	0.11193681039	0.412827466554	0.328903473203	0.0646173544015	0.342660318602	0.172852100879	-0.214702082332	-0.694571858503	0.640507910251	-0.0839768502123	-0.0141035197332	0.907680890566	0.0373091627142	0.703288656696	-0.568552902174	6.28607569843	54.824882422
15	1.67650667218	0.0523404193133	-1.10838354939	1.02543944629	0.620814695946	5.99342247293	-0.228000612858	0.0957207923852	0.277468438964	-0.363170253766	0.792320401303	0.173558800868	0.378338750056	-0.748247655315	-0.496840045269	0.899471602505	-0.0993925531041	0.0530692337862	1.08068072445	0.0278400863466	0.897738403172	-14.5717402547	2.19201800781	78.0824065925
16	5.09325089488	0.213361025341	-1.11320464	6.36916349961	1.66662902331	4.08803056363	0.170764786621	1.07704442565	-1.4490459451	-0.546514723269	0.0750893536828	-0.286961470216	0.896178990427	0.483447764988	-0.307878642174	0.691627991647	-0.00415848260463	-0.0182327340247	0.84209961646	-0.267341152794	0.911028307007	-11.2425668216	-14.828814797	23.814220697

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 8 )	A	A	-1 - 8
2	2	chain 'A' and (resid 9 through 28 )	A	A	9 - 28
3	3	chain 'A' and (resid 29 through 38 )	A	A	29 - 38
4	4	chain 'A' and (resid 39 through 68 )	A	A	39 - 68
5	5	chain 'A' and (resid 69 through 73 )	A	A	69 - 73
6	6	chain 'A' and (resid 74 through 82 )	A	A	74 - 82
7	7	chain 'B' and (resid 3 through 207 )	B	B	3 - 207	1 - 205
8	8	chain 'B' and (resid 208 through 411 )	B	B	208 - 411	206 - 407
9	9	chain 'B' and (resid 412 through 730 )	B	B	412 - 730	408 - 723
10	10	chain 'B' and (resid 731 through 888 )	B	B	731 - 888	724 - 872
11	11	chain 'B' and (resid 889 through 1366 )	B	B	889 - 1366	873 - 1326
12	12	chain 'C' and (resid -7 through -3 )	C	C	-7 - -3
13	13	chain 'C' and (resid -2 through 2 )	C	C	-2 - 2
14	14	chain 'C' and (resid 3 through 12 )	C	C	3 - 12
15	15	chain 'C' and (resid 13 through 20 )	C	C	13 - 20
16	16	chain 'D' and (resid -3 through 7 )	D	D	-3 - 7

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