PDB-7qqr: SpCas9 bound to AAVS1 off-target5 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qqr

Title

SpCas9 bound to AAVS1 off-target5 DNA substrate

Components

(AAVS1 off-target5 ...) 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: 2.75 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	7qqr.cif.gz	837.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qqr_validation.pdf.gz	484 KB	Display	wwPDB validaton report
Full document	7qqr_full_validation.pdf.gz	498.9 KB	Display
Data in XML	7qqr_validation.xml.gz	51.1 KB	Display
Data in CIF	7qqr_validation.cif.gz	72.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqr ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqr	HTTPS FTP

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Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqsC 7qqtC 7qquC 7qqvC 7qqwC 7qqxC 7qqzC 7qr0C 7qr1C 7qr5C 7qr7C 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-target5 target strand

D: AAVS1 off-target5 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)	178.637, 67.027, 187.803
Angle α, β, γ (deg.)	90.000, 111.345, 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-target5 ... , 2 types, 2 molecules CD

#3: DNA chain	AAVS1 off-target5 target strand Mass: 8487.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	AAVS1 off-target5 non-target strand Mass: 3709.413 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: 27266.279 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

AAVS1 sgRNA

Mass: 27266.279 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 , 4 types, 238 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: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 218 / 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: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.75→46.26 Å / Num. obs: 53929 / % possible obs: 99.2 % / Redundancy: 6.9 % / B_iso Wilson estimate: 69.74 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.19 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.75→2.85 Å / Redundancy: 7.2 % / R_merge(I) obs: 2.15 / Mean I/σ(I) obs: 1 / Num. unique obs: 5348 / CC_1/2: 0.343 / % possible all: 99.7

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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: 2.75→47.7 Å / SU ML: 0.4178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2309	2704	5.02 %
R_work	0.189	51203	-
obs	0.1912	53907	99.22 %

Solvent computation

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

Displacement parameters

B_iso mean: 82.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→47.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10905	2552	35	218	13710

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	13969
X-RAY DIFFRACTION	f_angle_d	0.6397	19355
X-RAY DIFFRACTION	f_chiral_restr	0.041	2207
X-RAY DIFFRACTION	f_plane_restr	0.0035	2032
X-RAY DIFFRACTION	f_dihedral_angle_d	17.4576	5663

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 (%)
2.75-2.8	0.3623	146	0.3272	2708	X-RAY DIFFRACTION	99.65
2.8-2.85	0.355	140	0.3125	2615	X-RAY DIFFRACTION	99.71
2.85-2.91	0.3362	152	0.3038	2717	X-RAY DIFFRACTION	99.76
2.91-2.98	0.3341	132	0.2908	2709	X-RAY DIFFRACTION	99.79
2.98-3.04	0.3948	145	0.309	2658	X-RAY DIFFRACTION	99.72
3.04-3.12	0.3506	136	0.2922	2669	X-RAY DIFFRACTION	99.43
3.12-3.21	0.3488	142	0.2675	2708	X-RAY DIFFRACTION	99.13
3.21-3.3	0.2967	142	0.2386	2646	X-RAY DIFFRACTION	99.04
3.3-3.41	0.2673	143	0.2163	2689	X-RAY DIFFRACTION	99.37
3.41-3.53	0.2861	150	0.2152	2701	X-RAY DIFFRACTION	99.17
3.53-3.67	0.2291	133	0.1984	2654	X-RAY DIFFRACTION	98.45
3.67-3.84	0.1956	136	0.1727	2642	X-RAY DIFFRACTION	97.17
3.84-4.04	0.1822	149	0.1574	2660	X-RAY DIFFRACTION	99.22
4.04-4.29	0.1713	135	0.1511	2697	X-RAY DIFFRACTION	99.51
4.29-4.62	0.1961	144	0.1471	2729	X-RAY DIFFRACTION	99.76
4.62-5.09	0.1957	142	0.1398	2740	X-RAY DIFFRACTION	99.83
5.09-5.82	0.2222	143	0.161	2713	X-RAY DIFFRACTION	99.62
5.82-7.33	0.2257	146	0.1853	2716	X-RAY DIFFRACTION	97.58
7.33-47.7	0.1855	148	0.1624	2832	X-RAY DIFFRACTION	99.33

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	0.619649136061	-0.740403566577	-0.672913726621	0.0761425008776	1.1447961328	2.80302958111	-0.110592770564	0.0358933591875	0.26946324162	0.280981030999	0.195292253275	-0.00467353311012	0.89731844596	-0.376365358722	-0.276747700419	0.682857846104	-0.116541377242	0.0703218005041	0.553369349744	-0.0523543093726	0.562037710256	-1.11712875331	4.59483808976	48.8544449252
2	0.0302941666311	0.071977717663	0.195028031648	0.647149620815	1.16222281254	2.32287833773	0.333270832782	0.841661213449	-0.326243903643	-0.721499598941	0.0906850493015	0.41655085193	0.508549120436	-0.209324188629	-0.316975435795	1.28563766945	0.235937537646	-0.192863052365	1.66676571411	-0.262430214036	1.03571691377	22.3431947633	-16.3533783239	1.68860324654
3	1.343404444	0.302612286444	0.619418250125	0.716213676138	0.0604030091875	1.20851187623	0.00349847498796	0.20774940667	0.0840620611008	-0.141517096921	-0.000474999929315	0.0771794045309	0.0530567618898	-0.0197609087942	-0.000236998051855	0.41889275698	-0.0450229768031	-0.0390705787683	0.395878033701	0.0325779884844	0.356816708626	1.09173293536	7.67358984181	28.1643091523
4	0.429174194622	-0.257052748049	-0.454417304858	0.163521123983	0.245489819214	1.24727184955	0.481484806352	-0.871255725729	0.916128943319	-0.125979483792	-0.305185315852	0.19644308257	-1.24499875986	0.605606120443	-0.230960826403	1.16923324999	-0.0855482201185	0.189684008638	0.995234121487	0.065756124577	1.16818920432	-40.2646184732	14.1825197605	34.0495118863
5	1.03026567573	-0.0283642080331	0.105143181468	0.210986158157	-0.291511272292	0.537212941093	-0.0399760985261	-0.00420311411395	0.0297618008486	0.0855953479762	-0.0669843467453	-0.0535225548109	0.0016932617631	0.146287157816	0.11515509058	0.453843449653	-0.0315884509344	0.00363483719565	0.362718780333	-0.0881035832328	0.398969362795	10.3843163102	3.64326697501	45.1954187504
6	0.491975264247	-0.2264952905	-0.294783332795	-0.0542328244208	0.172150698676	1.62844087957	-0.0396020601264	-0.033480732918	0.0224963369195	0.140051174458	0.019105180367	-0.0462963075239	-0.0119772796892	0.182406562723	0.0199474320542	0.512059653461	-0.052519107018	-0.0386602316958	0.364831898494	0.0369012918309	0.511290127393	10.2984078436	10.7502738038	58.4505742805
7	0.286459057023	0.107500938718	0.505113667116	0.546304044308	0.0349666209502	0.800618771855	0.046679739904	-0.0340682262959	-0.113608386432	0.112290224071	-0.00897827193606	-0.144255162506	0.226639100706	0.10336288357	-0.0307785790293	0.60587015099	0.00842831295627	0.062212031622	0.667486775828	-0.00647537155505	0.699943583081	-10.6988146334	-6.36941369559	66.4618889567
8	1.28096977405	0.225294026538	-0.463794400875	0.479407031429	-0.113217563231	1.36383825562	-0.0747640033281	0.0381713917853	-0.192432759593	0.0194767186044	0.0941807922727	0.00446498169	0.364277936143	-0.188441627897	-0.0212492695633	0.50621764144	-0.0991302609539	-0.0196598834151	0.449616127766	-0.00750765225438	0.568069257952	-29.8492888678	-12.043769437	43.3563946631
9	3.53579813425	0.504195005134	0.872258365711	1.89952050774	-0.18825398903	3.16108831746	0.00272006387453	0.394300386277	0.0202731649436	-0.306809460171	-0.351486748912	0.562371409946	0.490365442419	-0.729192247574	0.330679242287	0.852864335011	-0.167247109445	-0.00572625253018	1.19602303253	-0.188448839811	0.820983867048	-9.58842558933	-14.8777820953	25.3090048339
10	1.583203442	0.118500784837	-2.0247273251	-0.0655607385892	0.0642161357439	3.97458881113	0.0622530039227	0.150317821484	0.429141033821	0.146320483619	0.439946401745	0.128149907976	0.492334059775	-0.496998030108	-0.598702321053	0.651610378134	-0.0683554013329	0.0502466308184	0.630307160548	0.0476182351424	0.572345273766	-7.55570362548	5.10627999813	65.242101447
11	5.32769296966	-0.726154914744	-2.4173672973	6.0937454384	0.687197003003	5.23263240649	0.369252458192	0.814635850668	-1.00275006048	-0.45693900759	0.423899189271	-0.423659213395	0.692377432482	0.147689615703	-0.912663040577	0.60150891516	-0.0910899802655	-0.0989932205859	0.746474635665	-0.193201362665	0.720388758931	-11.906578742	-14.5554655542	23.3715585541

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 82 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 286 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 287 through 678 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 679 through 909 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 910 through 1366 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid -7 through 2 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 20 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid -2 through 7 )

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