PDB-7qqp: SpCas9 bound to AAVS1 off-target3 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qqp

Title

SpCas9 bound to AAVS1 off-target3 DNA substrate

Components

(AAVS1 off-target3 ...) 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: 2.6 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	7qqp.cif.gz	844.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qqp_validation.pdf.gz	486.8 KB	Display	wwPDB validaton report
Full document	7qqp_full_validation.pdf.gz	504.5 KB	Display
Data in XML	7qqp_validation.xml.gz	51.6 KB	Display
Data in CIF	7qqp_validation.cif.gz	73.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqp ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqp	HTTPS FTP

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Related structure data

Related structure data	7qqoC 7qqqC 7qqrC 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-target3 target strand

D: AAVS1 off-target3 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)	177.606, 67.730, 188.090
Angle α, β, γ (deg.)	90.000, 111.267, 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-target3 ... , 2 types, 2 molecules CD

#3: DNA chain	AAVS1 off-target3 target strand Mass: 8357.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	AAVS1 off-target3 non-target strand Mass: 3757.463 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, 260 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.: 10 / Source method: obtained synthetically / Formula: K
#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 244 / 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: Oct 22, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→46.29 Å / Num. obs: 64238 / % possible obs: 99.4 % / Redundancy: 7.1 % / B_iso Wilson estimate: 66.57 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.12 / Net I/σ(I): 11
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 7.3 % / R_merge(I) obs: 1.76 / Mean I/σ(I) obs: 1 / Num. unique obs: 6396 / CC_1/2: 0.453 / % possible all: 99.6

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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→47.96 Å / SU ML: 0.3945 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2249	3220	5.01 %
R_work	0.1941	60993	-
obs	0.1957	64213	99.38 %

Solvent computation

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

Displacement parameters

B_iso mean: 84.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→47.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10902	2550	28	244	13724

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	13966
X-RAY DIFFRACTION	f_angle_d	0.5297	19353
X-RAY DIFFRACTION	f_chiral_restr	0.0371	2208
X-RAY DIFFRACTION	f_plane_restr	0.0029	2034
X-RAY DIFFRACTION	f_dihedral_angle_d	17.0566	5667

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	0.3866	143	0.3553	2674	X-RAY DIFFRACTION	99.93
2.64-2.68	0.3652	139	0.3283	2576	X-RAY DIFFRACTION	99.27
2.68-2.72	0.3214	136	0.32	2674	X-RAY DIFFRACTION	99.82
2.72-2.77	0.3554	139	0.3028	2588	X-RAY DIFFRACTION	99.24
2.77-2.82	0.3197	140	0.2874	2673	X-RAY DIFFRACTION	99.96
2.82-2.88	0.3191	139	0.2789	2637	X-RAY DIFFRACTION	99.5
2.88-2.93	0.3149	140	0.2716	2641	X-RAY DIFFRACTION	99.78
2.93-3	0.2746	142	0.2654	2626	X-RAY DIFFRACTION	99.96
3-3.07	0.2817	136	0.2726	2685	X-RAY DIFFRACTION	99.82
3.07-3.14	0.3031	139	0.2538	2617	X-RAY DIFFRACTION	99.64
3.14-3.23	0.2668	141	0.2307	2648	X-RAY DIFFRACTION	99.86
3.23-3.32	0.2743	140	0.2171	2625	X-RAY DIFFRACTION	99.57
3.32-3.43	0.2594	137	0.2093	2658	X-RAY DIFFRACTION	99.64
3.43-3.55	0.2456	142	0.2083	2654	X-RAY DIFFRACTION	98.52
3.55-3.7	0.2403	136	0.1943	2568	X-RAY DIFFRACTION	97.65
3.7-3.86	0.2156	139	0.1816	2634	X-RAY DIFFRACTION	98.44
3.86-4.07	0.1906	144	0.1686	2677	X-RAY DIFFRACTION	100
4.07-4.32	0.2026	139	0.1591	2671	X-RAY DIFFRACTION	99.89
4.32-4.66	0.1883	139	0.1524	2659	X-RAY DIFFRACTION	99.57
4.66-5.12	0.1854	142	0.1519	2682	X-RAY DIFFRACTION	99.68
5.13-5.87	0.2038	141	0.1673	2696	X-RAY DIFFRACTION	99.75
5.87-7.39	0.2064	141	0.1897	2647	X-RAY DIFFRACTION	97.11
7.39-47.96	0.1738	146	0.1614	2783	X-RAY DIFFRACTION	99.32

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	0.78924634209	0.240478366553	0.279213313621	0.785461777598	1.29078974989	3.39129137941	-0.227497255688	-0.00289804435492	0.0167834665075	0.333056712446	0.144509483272	0.149131048024	1.11801086564	-0.491343626146	0.00674285767341	0.712502292319	-0.112885145648	0.0737879004138	0.461280851481	-0.0480820512462	0.561865006529	-7.4422869042	6.22667551489	61.1901076864
2	1.46481733627	-0.110872299989	1.16727102523	1.03907607582	0.0842451835874	0.809987323933	0.341195486372	0.883125728995	0.00527622124679	-0.234352440067	0.0215682221397	-0.413902348016	0.796573835278	0.570946786937	-0.0838781592775	0.684454278981	0.172432154998	-0.0266253948932	0.943488026625	-0.0851644556983	0.564927602391	18.4084601307	-5.85018133143	13.209230771
3	1.09358835895	-0.757456043428	0.103547774672	2.00433589178	0.784448797746	2.02255727844	0.446834731972	0.742579317535	-0.350269243474	-0.281580197884	-0.210888229969	-0.157210192732	0.900049951973	0.282212414587	-0.149968606588	0.791604229877	0.1814757217	-0.132217078045	0.918709511718	-0.190177240186	0.682889588143	19.805429869	-8.81808285447	15.6700017594
4	1.25441074189	0.0931492883896	0.696178252149	-0.0904629111026	0.153313135525	1.15404726508	0.0623349009231	-0.0864867243814	0.43499200287	-0.0636261835614	-0.113588686127	0.27807187509	-0.215927010015	-0.0869054862816	-0.00603918338357	0.408646085195	-0.0617015874535	-0.0432853794133	0.388723537658	0.00655526801263	0.549943036956	-11.1460846797	14.0973288474	32.8386265494
5	0.0559397939391	-0.491077551926	-0.039465624931	4.58449783095	1.01567038165	0.647760859555	0.589797614636	-0.0893681551248	1.65450112874	-0.380844135734	-0.0503839351719	-0.245987504838	-1.99582524136	1.66933522935	-0.49461939223	1.46001602496	-0.0998024260741	0.150977969745	1.05071755535	0.26008745627	1.55313654655	-38.6371660956	17.122163819	29.5395526671
6	4.29555786685	2.96916116255	-2.0389729804	3.58887977363	-0.906405501464	1.86668875632	0.441208918288	-0.791099708811	0.0444892852867	0.336921729797	0.276869107559	-0.189242107723	-0.495629926497	0.478265631321	-0.49759110499	1.00048267074	-0.118202368332	0.203963543497	1.21495263274	-0.0688521627332	0.928568285697	-40.7862183098	12.807882289	37.9501050129
7	1.21518488551	0.324680729457	0.0368644685853	0.392004323013	-0.267267370756	1.09235086431	0.0637175850262	0.117349441986	0.0787783228111	0.11916018619	-0.097608918668	-0.0254503011996	-0.043744938309	0.313070444826	0.0560239595872	0.461580146073	-0.0742616520718	-0.0264395806708	0.373354423923	-0.0625645793638	0.454704925132	6.12240847379	6.03982840007	37.3811283743
8	0.461213899119	0.23105710887	1.35556977695	0.15573874027	-1.39611494364	3.15746183628	0.076087308164	-0.0436731123992	-0.0878184976109	0.258718345417	-0.0928566101223	0.111994412024	-0.0071940448263	-0.0412607250502	0.0330438756442	0.743013942932	0.193851673706	-0.036320332302	0.740509203777	-0.0294748129061	0.645147445152	24.4640178531	-7.57650588688	49.8087784425
9	0.562528920418	-0.148254734376	-0.252849378012	0.346241558354	0.233926865157	2.17548290417	-0.0102890101819	-0.0935096489089	0.106445281422	0.217565534775	0.0680237627838	-0.0544383623732	-0.210115861221	0.162065013332	-0.0411585266675	0.523856150393	-0.0566838183777	-0.0419463327234	0.307661882622	-0.00671016777784	0.505591741209	2.27152420629	17.5333121143	66.9767490319
10	0.57505311885	-0.349975397101	0.364880179979	1.61163125478	-0.161800060843	1.62767265017	-0.0426299333119	-0.138292474129	-0.0895875679717	0.403126112693	0.000373289384262	-0.569045918489	0.395863246296	0.267519059359	-0.0739728315858	0.71440412072	-0.0203901002468	-0.0508011077673	0.628365847354	0.0550362589477	0.803343541768	-14.9148854219	-11.8792236945	64.3375240543
11	1.3523984057	0.248941061819	-0.421939811911	0.672833529746	-0.100810936847	1.67060184303	-0.129424127802	0.070448762393	-0.237445564322	0.0492661097974	0.0951390432313	0.0630332939635	0.594186483421	-0.291215773959	0.0404970783377	0.581991893225	-0.171920589065	0.0193834119022	0.436268498651	-0.0487707571134	0.558880658927	-28.7468109935	-13.9111696928	39.4601012715
12	5.33271127684	0.709214725652	1.48469054157	1.8186949887	-0.176724612163	2.60548082231	-0.299929206403	0.968426476973	-0.145276845862	-0.196217878036	0.163392087092	0.685519409659	-0.0136866969975	-1.37767212235	0.18527042429	1.35729164181	-0.619813400638	0.0392503357495	2.07161832447	-0.671139065226	1.2661261888	-15.8436492629	-20.793576338	18.6760620592
13	1.29183865373	0.846031803247	-0.138058717058	2.91336115751	0.648556651963	0.81731219788	-0.321472840798	-0.408919173019	-0.0133147267305	0.0530713566354	-0.0304130523284	0.215610685776	-0.0805765113892	0.546347803061	0.352455803224	0.601513432105	-0.102641028034	-0.0388180067301	0.52670848904	-0.108476054261	0.585079499538	-2.25913877351	-10.0400406449	30.9861037837
14	0.702240282061	0.470680207773	-0.211098842885	0.227166552791	-0.338209046596	2.11928509212	-0.0158089436954	0.145196030801	0.176395073272	0.122151153467	0.35690361647	0.222139394417	0.719882077049	-0.372486689814	-0.291200273551	0.674283211109	-0.146635345404	0.0770715436229	0.4880437359	0.0455031496961	0.485060777808	-7.37569086509	4.89465748913	65.5940556216
15	4.51861165297	0.0441895651079	-1.57927577548	5.02859925519	0.610572601405	4.22072103034	-0.0536076891745	0.698994237813	-1.13505687083	-0.284329910215	0.274118934085	-0.422594705783	1.13153325201	0.316083380132	-0.538620561702	0.715085136478	-0.0924929211754	-0.0250434375809	0.647458327428	-0.274241780929	0.847311796249	-11.2678485841	-14.5851696686	23.9447620081

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 34 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 35 through 49 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 50 through 69 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 70 through 74 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 75 through 82 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 207 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 208 through 382 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 383 through 730 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 731 through 980 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 981 through 1366 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid -7 through -3 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -2 through 2 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 3 through 20 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid -2 through 7 )

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