PDB-7qqt: SpCas9 bound to FANCF off-target1 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qqt

Title

SpCas9 bound to FANCF off-target1 DNA substrate

Components

(FANCF off-target1 ...) x 2
CRISPR-associated endonuclease Cas9/Csn1
FANCF 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: 2.5 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	7qqt.cif.gz	842.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qqt_validation.pdf.gz	472.9 KB	Display	wwPDB validaton report
Full document	7qqt_full_validation.pdf.gz	489.2 KB	Display
Data in XML	7qqt_validation.xml.gz	55.5 KB	Display
Data in CIF	7qqt_validation.cif.gz	81 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqt ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqt	HTTPS FTP

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Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqrC 7qqsC 7qquC 7qqvC 7qqwC 7qqxC 7qqzC 7qr0C 7qr1C 7qr5C 7qr7C 7qr8C 7zo1C 5fq5S 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: FANCF sgRNA

B: CRISPR-associated endonuclease Cas9/Csn1

C: FANCF off-target1 target strand

D: FANCF off-target1 non-target strand

hetero molecules

198 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)	177.591, 66.733, 187.020
Angle α, β, γ (deg.)	90.000, 111.028, 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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FANCF off-target1 ... , 2 types, 2 molecules CD

#3: DNA chain	FANCF off-target1 target strand Mass: 8622.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	FANCF off-target1 non-target strand Mass: 3662.404 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	FANCF sgRNA Mass: 27068.125 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

FANCF sgRNA

Mass: 27068.125 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, 633 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 621 / 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: Oct 7, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→47.58 Å / Num. obs: 71236 / % possible obs: 99.9 % / Redundancy: 6.8 % / B_iso Wilson estimate: 46.14 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.19 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 6.8 % / R_merge(I) obs: 1.76 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7053 / CC_1/2: 0.4 / % 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: 2.5→47.58 Å / SU ML: 0.387 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2376	3562	5 %
R_work	0.2028	67639	-
obs	0.2046	71201	99.93 %

Solvent computation

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

Displacement parameters

B_iso mean: 60.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→47.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10889	2534	12	621	14056

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	13916
X-RAY DIFFRACTION	f_angle_d	0.5335	19290
X-RAY DIFFRACTION	f_chiral_restr	0.0381	2200
X-RAY DIFFRACTION	f_plane_restr	0.003	2030
X-RAY DIFFRACTION	f_dihedral_angle_d	16.9046	5641

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 (%)
2.5-2.53	0.378	131	0.3297	2637	X-RAY DIFFRACTION	99.93
2.53-2.57	0.3496	155	0.3313	2727	X-RAY DIFFRACTION	99.93
2.57-2.61	0.3504	141	0.3244	2647	X-RAY DIFFRACTION	100
2.61-2.65	0.3699	141	0.3156	2692	X-RAY DIFFRACTION	99.96
2.65-2.69	0.3574	132	0.3029	2692	X-RAY DIFFRACTION	100
2.69-2.74	0.3478	149	0.2957	2692	X-RAY DIFFRACTION	99.96
2.74-2.79	0.3125	137	0.2858	2739	X-RAY DIFFRACTION	100
2.79-2.84	0.3209	143	0.2751	2625	X-RAY DIFFRACTION	99.96
2.84-2.9	0.3165	152	0.2649	2720	X-RAY DIFFRACTION	99.97
2.9-2.96	0.3099	138	0.2541	2701	X-RAY DIFFRACTION	99.96
2.96-3.03	0.2969	142	0.2622	2675	X-RAY DIFFRACTION	100
3.03-3.11	0.3114	139	0.2567	2684	X-RAY DIFFRACTION	99.93
3.11-3.19	0.3099	139	0.2435	2720	X-RAY DIFFRACTION	99.93
3.19-3.29	0.2596	144	0.2272	2666	X-RAY DIFFRACTION	99.96
3.29-3.39	0.2514	141	0.2059	2704	X-RAY DIFFRACTION	99.96
3.39-3.51	0.2348	151	0.2027	2739	X-RAY DIFFRACTION	99.97
3.51-3.65	0.2224	133	0.1859	2669	X-RAY DIFFRACTION	99.93
3.65-3.82	0.1931	141	0.1802	2720	X-RAY DIFFRACTION	99.83
3.82-4.02	0.1912	151	0.1679	2675	X-RAY DIFFRACTION	99.93
4.02-4.27	0.1835	135	0.1584	2715	X-RAY DIFFRACTION	99.89
4.27-4.6	0.1815	144	0.1517	2728	X-RAY DIFFRACTION	99.97
4.6-5.07	0.1883	144	0.1465	2729	X-RAY DIFFRACTION	99.97
5.07-5.8	0.2288	143	0.168	2740	X-RAY DIFFRACTION	99.93
5.8-7.3	0.2026	147	0.1835	2769	X-RAY DIFFRACTION	99.97
7.3-47.58	0.1886	149	0.165	2834	X-RAY DIFFRACTION	99.57

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	0.1267029748	0.0199502041774	0.301630453409	0.200919986391	0.218507394687	0.355952424155	-0.0428874477597	-0.0485688358925	0.128494801321	-0.0334953889007	-0.05518842618	0.0891115628792	0.477688020438	-0.0414611695758	-0.00129601872548	0.393865896388	-0.081673544817	0.0581521870466	0.39265825109	-0.0553460614421	0.395791131832	-8.20228475504	7.07543400446	62.1387644484
2	0.1781962996	0.0981588186699	-0.144412795132	0.16218117915	-0.210523659394	0.238994985209	0.180677227862	0.350498794878	0.212237884022	0.0722846088896	0.141941277935	0.0536237625056	0.320677383001	0.219100695896	0.175103122846	0.39773536187	0.0932970756346	-0.0950795066202	0.571822870444	-0.080824205569	0.320452483822	17.9343919289	-4.10597331613	16.1806615027
3	0.00155582274897	0.0012931836926	0.00465269350301	0.0107672700278	0.00632074476536	0.00795471330425	0.00194920315665	0.0911423027795	0.119115098112	-0.245431116843	-0.0325300761005	0.191182476793	-0.0258279894246	-0.0390438072293	7.25638885733E-5	1.06191070088	0.200316425965	-0.2271059324	1.10074985861	-0.098048928301	0.851806260927	18.5591543864	-19.1429174219	-0.628036601656
4	0.226341877366	0.259100465143	0.231809316409	0.23035078273	0.0838421682389	0.552156236384	0.0648570716809	0.0524259830445	0.0955588980056	-0.0168448519342	0.0512252191703	0.0373299979343	-0.0203335320541	0.0630983265057	1.41566513887E-5	0.279387626876	-0.0390756307829	-0.0249870834774	0.300347672867	0.0180179176369	0.318757743366	1.36222433503	7.73596914305	28.1776888866
5	0.0435205090752	-0.0428651567808	0.031402438244	0.056814939921	0.0149553997005	0.0331130036926	0.345794657629	0.0187420924981	0.126079218249	-0.191676078773	-0.0207976397059	0.0636028458549	-0.541025999394	0.188263573739	0.000229541596658	0.604512198415	-0.137229957569	0.107705719739	0.67875582906	0.130912447122	0.718521991548	-39.2069535517	14.8779147124	33.611451065
6	0.373569264198	0.21285352095	-0.0607991467606	0.103658121851	-0.138062118479	0.470216345931	0.0949618968416	0.128209620511	-0.00897236596828	0.0464239688632	-0.0713234866909	0.0178194950525	-0.0541621020432	0.111420287	0.0018478542828	0.246271278855	-0.0520631806316	0.00312209452901	0.23607603648	-0.0194322080149	0.274196638042	5.67441595172	6.44247323928	37.2882943651
7	0.187342433829	-0.253166359029	0.351018229376	0.150317850137	-0.352032080443	0.309470647831	-0.0565680350548	0.117663238536	-0.0966032860724	0.170415080064	-0.121618466397	0.089341636143	-0.0999896140916	-0.136093422712	7.89780864496E-6	0.478038536798	0.0476837292127	0.0142745820933	0.392648913691	-0.0297615993748	0.443562550178	26.3024018172	-3.43774749367	56.2826109997
8	0.811789650095	-0.096310322808	-0.104394239054	0.327822759411	0.0524007088052	0.745825794702	0.0684499608915	-0.106095154796	-0.052833046326	0.102538510604	-0.0187052419907	0.0441014343649	-0.00252603706677	0.22827154028	-1.19618722092E-5	0.28498736742	-0.0238275150404	-0.0429618711708	0.303871348631	0.028703776039	0.280735007689	16.2116760188	5.93202656643	37.3364054752
9	0.188926348465	0.134784007692	0.229934005843	0.385340891057	0.00813413689292	0.476977377973	-0.0937146246251	0.0403744712446	-0.0530804316617	0.06078424035	0.0526368156738	-0.0462833774893	-0.0701225146575	-0.00776349462928	6.37358147169E-6	0.292341929828	0.00780569384724	0.0190630388367	0.285990266025	-0.0161150097198	0.290387622703	-6.00486431079	13.5732376994	73.2103701443
10	0.109667116365	-0.027451028855	-0.0460915668686	0.294221216367	-0.0655505916768	0.130494172085	-0.00986791844202	0.00472607188527	-0.0203152736473	-0.0499317464085	-0.0765285084739	0.155894455766	0.000542133853716	0.0568218207557	-1.1374996656E-8	0.600184373026	-0.0103321918108	-0.0496351462989	0.681228316727	-0.000479742752108	0.69180475986	-2.92787877902	-18.8774462116	71.2740593743
11	0.657527496972	0.127242021036	-0.253855935474	0.236456769634	-0.0340237075603	0.855014286167	-0.0861212192249	0.0803007170455	-0.0458062063566	0.0152104276926	0.0501476715735	0.000380823758539	0.268817979359	-0.137058223897	-0.000582526769273	0.295345987375	-0.0901134923749	0.00191932938863	0.172930903837	-0.0183558905306	0.255293191253	-29.296290598	-11.6839502325	42.9304599881
12	0.0187673767334	0.0766436114954	-0.0693617720927	0.012100510395	-0.0407900821857	0.069018239373	0.00363233257869	0.415760711891	-0.342505375117	0.00506267499768	-0.230958769608	0.0277240299469	0.183556741662	-0.344269459859	-0.00947163230613	0.45228144582	-0.111582408978	-0.0149605454729	0.645220459777	-0.218736377035	0.556384258268	-8.80450014924	-15.2036946729	25.2351270756
13	-0.000831369884639	0.00900592899803	0.093088520538	-0.0536420455191	0.148014440654	0.0851564649974	0.0395362027522	-0.0403671142688	0.220435453811	0.0246629619416	0.19464057137	0.0285858606354	0.241144082141	0.0451977872646	-2.47199329483E-5	0.412030908369	-0.0418748256799	0.0362970854935	0.407378835284	0.0178366705359	0.344878927646	-6.99346984361	5.31934346628	65.1393143717
14	0.105061304607	-0.0636819371071	-0.033118464586	0.306298140828	-0.154389260822	0.150136510807	0.0950453461159	0.374502478054	-0.743479023618	-0.00559316037742	0.171500227984	0.0643567503674	0.183555239027	-0.0108532842918	0.135112013443	0.517266768233	-0.0687644675506	-0.00568014625106	0.411332088171	-0.210752726447	0.596428704791	-11.5281708668	-14.3527385069	23.8124221712

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 38 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 39 through 68 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 69 through 82 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 207 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 208 through 342 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 343 through 493 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 494 through 808 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 809 through 909 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 910 through 1367 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid -7 through 2 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 3 through 20 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid -2 through 7 )

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