PDB-7zo1: SpCas9 bound to CD34 off-target9 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7zo1

Title

SpCas9 bound to CD34 off-target9 DNA substrate

Components

(CD34 off-target9 DNA ...) x 2
CD34 sgRNA
CRISPR-associated endonuclease Cas9/Csn1

Keywords

HYDROLASE / CRISPR / Cas9 / off-target / ternary / deletion

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: 2.4 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	Apr 23, 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 / _citation_author.identifier_ORCID / _citation_author.name
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	7zo1_validation.pdf.gz	445.1 KB	Display	wwPDB validaton report
Full document	7zo1_full_validation.pdf.gz	455.6 KB	Display
Data in XML	7zo1_validation.xml.gz	25.4 KB	Display
Data in CIF	7zo1_validation.cif.gz	40.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zo/7zo1 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/7zo1	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 7qr7C 7qr8C 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: CD34 sgRNA

B: CRISPR-associated endonuclease Cas9/Csn1

C: CD34 off-target9 DNA target strand

D: CD34 off-target9 DNA 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)	177.410, 69.200, 188.460
Angle α, β, γ (deg.)	90.000, 111.770, 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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CD34 off-target9 DNA ... , 2 types, 2 molecules CD

#3: DNA chain	CD34 off-target9 DNA target strand Mass: 8394.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	CD34 off-target9 DNA non-target strand Mass: 3716.451 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	CD34 sgRNA Mass: 27598.482 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 (E. coli) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

#1: RNA chain

CD34 sgRNA

Mass: 27598.482 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 (E. coli)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 294 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.: 8 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 284 / 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: 53.33 % / Description: Plates
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: Mar 18, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→46.51 Å / Num. obs: 83421 / % possible obs: 99.79 % / Redundancy: 6.8 % / B_iso Wilson estimate: 57.51 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.1336 / Net I/σ(I): 10.29
Reflection shell	Resolution: 2.4→2.486 Å / Redundancy: 6.7 % / R_merge(I) obs: 2.538 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 8284 / CC_1/2: 0.385 / % possible all: 99.63

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FQ5

5fq5

Resolution: 2.4→46.51 Å / SU ML: 0.3974 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.1692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2496	4161	4.99 %
R_work	0.2118	79174	-
obs	0.2137	83335	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 90.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→46.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9553	2554	21	273	12401

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	12604
X-RAY DIFFRACTION	f_angle_d	0.5131	17548
X-RAY DIFFRACTION	f_chiral_restr	0.0362	2011
X-RAY DIFFRACTION	f_plane_restr	0.0037	1793
X-RAY DIFFRACTION	f_dihedral_angle_d	14.2202	5115

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 (%)
2.4-2.43	0.3465	132	0.3445	2600	X-RAY DIFFRACTION	99.67
2.43-2.46	0.3876	133	0.3643	2642	X-RAY DIFFRACTION	99.64
2.46-2.49	0.4359	144	0.365	2615	X-RAY DIFFRACTION	99.67
2.49-2.52	0.3635	139	0.349	2598	X-RAY DIFFRACTION	99.89
2.52-2.55	0.3828	128	0.3384	2627	X-RAY DIFFRACTION	99.86
2.55-2.59	0.3826	133	0.3259	2633	X-RAY DIFFRACTION	99.96
2.59-2.62	0.3457	154	0.3187	2610	X-RAY DIFFRACTION	99.82
2.62-2.66	0.3971	124	0.303	2648	X-RAY DIFFRACTION	99.82
2.66-2.7	0.3713	137	0.302	2574	X-RAY DIFFRACTION	99.89
2.7-2.75	0.3404	142	0.2983	2649	X-RAY DIFFRACTION	99.96
2.75-2.79	0.3302	142	0.2885	2646	X-RAY DIFFRACTION	99.86
2.79-2.85	0.3221	143	0.277	2588	X-RAY DIFFRACTION	99.85
2.85-2.9	0.3546	128	0.2834	2662	X-RAY DIFFRACTION	99.96
2.9-2.96	0.3464	143	0.2893	2624	X-RAY DIFFRACTION	99.89
2.96-3.02	0.3084	131	0.288	2630	X-RAY DIFFRACTION	99.93
3.02-3.09	0.3081	148	0.2704	2623	X-RAY DIFFRACTION	99.82
3.09-3.17	0.3409	139	0.2355	2647	X-RAY DIFFRACTION	99.79
3.17-3.26	0.2461	139	0.2089	2612	X-RAY DIFFRACTION	99.78
3.26-3.35	0.2457	133	0.2039	2627	X-RAY DIFFRACTION	99.78
3.35-3.46	0.2373	148	0.2171	2640	X-RAY DIFFRACTION	99.86
3.46-3.58	0.2617	130	0.2073	2649	X-RAY DIFFRACTION	99.64
3.58-3.73	0.2455	142	0.1963	2613	X-RAY DIFFRACTION	99.89
3.73-3.9	0.2116	143	0.185	2671	X-RAY DIFFRACTION	99.96
3.9-4.1	0.2066	134	0.177	2662	X-RAY DIFFRACTION	99.79
4.1-4.36	0.2315	144	0.1685	2631	X-RAY DIFFRACTION	99.86
4.36-4.7	0.2254	139	0.1629	2649	X-RAY DIFFRACTION	99.79
4.7-5.17	0.1915	139	0.156	2653	X-RAY DIFFRACTION	99.71
5.17-5.91	0.2226	144	0.1746	2684	X-RAY DIFFRACTION	99.68
5.92-7.45	0.2058	141	0.1998	2693	X-RAY DIFFRACTION	99.79
7.45-46.51	0.204	145	0.1898	2774	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	0.253423323203	0.179673500255	0.485205868614	0.562711341686	0.361795589765	0.817494306514	0.0143220749795	-0.365751435656	0.299861753657	0.0492571907174	0.524354718018	0.516394257542	0.962597268285	-0.0127567066802	0.00785080015952	0.776670913056	-0.0642670654202	0.178590614732	0.720072418228	0.0220605686707	0.776105291794	-9.16859087071	3.79370423021	64.1440848741
2	0.506378539929	0.0397915016368	0.592260582687	0.682144160999	0.130984672179	1.47665416705	0.19355300331	0.213417219486	0.258755799405	-0.0611595461441	-0.0409495359596	-0.164488537512	0.17830587465	0.377369659987	0.122495730917	0.447246184308	-0.0827316153035	-0.0452926584342	0.517178850098	-0.0656214851822	0.42044747257	9.02467649981	0.525801950498	22.121105325
3	0.862422312208	0.512413067331	0.93482664241	0.641785534987	0.471857708772	1.03411084843	0.0275686129834	-0.119528258479	0.969096641096	-0.0416262632306	0.0195967949911	0.303785704004	-0.925766142767	0.144758005047	0.170395346937	0.704239726567	-0.36249353545	0.0684840813275	0.674595276352	-0.0865285335796	1.01846003381	-37.7613461609	11.2844661427	36.0895275195
4	0.820166758369	0.094114703338	0.209946518087	0.18889170446	-0.0330478693782	0.960255014533	0.0800429698216	0.133949007727	0.0840324620612	0.0354569004158	-0.0280704180953	0.0148696847076	-0.0190609364556	0.150224726231	0.0588209030955	0.410980621826	-0.132022354619	-0.0106571751101	0.402183669217	-0.099459181301	0.462656635435	-0.808683869601	5.9585013665	31.358402996
5	0.32483422013	0.0778938483816	-0.0884047103271	0.0264064745359	-0.107840795178	0.116905297484	-0.147358850826	0.27256493488	-0.0782591218133	0.364364208647	-0.123327462443	0.250496083928	-0.0247929769911	0.581299074095	-8.03856595832E-5	0.79168637612	-0.11061810723	0.0960685399104	0.819127280098	-0.0495118345182	0.58002009955	31.7794013211	-3.8370669668	60.2065116056
6	0.565454200299	-0.189024228449	-0.170871247388	1.00754970002	-0.397816370787	1.45007558697	0.105825331031	-0.165827766626	0.0210489615525	0.580760780153	-0.0895851180117	0.0575214915753	0.184390499109	0.830675385995	0.0555306180991	0.503970786768	-0.0522387133081	-0.0412171651798	0.662662405021	-0.00397509864799	0.401178036131	24.6054323553	-3.06530988138	43.5410064909
7	0.8892023643	0.0191624394349	0.150957765667	1.23952058278	-0.630189068131	1.16900956267	-0.0403282481261	-0.0580589332765	-0.168780027463	0.771213142899	0.152310779523	0.104347218484	-0.689639331805	-0.188333580094	0.11598470461	0.985167113461	-0.0785579469132	0.114931647908	0.308914077099	-0.0239081586743	0.520395173076	-3.97378408503	18.5319047142	74.3051935281
8	1.3404087463	0.0729354618107	-0.36142637067	0.596767273626	-0.121929381795	0.946585712301	-0.0697613237386	0.0452973346259	-0.146097854308	0.12268737553	0.105622387477	0.0906606466575	0.25146944775	-0.370582971569	0.123802288909	0.544000784394	-0.306108172046	-0.00150311867247	0.467538366963	-0.0770277790078	0.435970002484	-29.801071019	-12.8050456278	42.3087816929
9	0.500106185209	-0.170273941772	0.145340614457	0.419404493258	-0.0566608982695	0.145271197892	-0.181515534477	0.229871404363	-0.00354424553738	0.0335883834838	-0.0592283049009	-0.114660249758	-0.00330768636132	-0.35258381634	-0.199575360619	1.03474499109	-0.629948916634	-0.123413746155	1.36400925138	-0.326576000384	0.947883611414	-15.567919123	-22.1138579333	18.8130378262
10	0.102052077965	0.184861520128	-0.12727835397	0.324263812888	-0.22807188163	0.158038197114	-0.0449459374087	0.0504379789179	-0.356234828981	0.113383959716	-0.395075129421	-0.0251290766465	0.0806668412139	0.0966134306637	-0.0377863165749	0.644611961869	-0.213763604663	-0.106279208638	0.443028443689	-0.0652775730408	0.57773808235	-2.20416072513	-10.7336657973	31.1896379758
11	0.203922231128	-0.0179726543272	-0.067738177147	0.0532924597586	-0.00351605688907	0.0180952401639	0.1728450455	0.163139712109	0.725811920435	0.251763773142	0.313849208709	0.0830427976856	0.763494271245	-0.0487371120858	0.00771613233444	0.738044527859	-0.222656000674	0.0652493260555	0.778499421333	-0.031479697781	0.621245889439	-0.626867790113	5.28125438151	55.1033223779
12	0.00343787036661	0.00320391271983	0.00566974089974	0.0120972500444	-0.0102462258794	0.0250243577596	-0.0235592058257	0.127062107804	0.352972681209	0.373550390685	0.267751433042	0.254793687836	0.0806691405362	-0.0504139702978	-0.000148156431819	2.12885525835	-0.0387156966718	0.291139170399	0.972989485059	0.36335837889	1.06283847122	-13.1885495722	-2.96682636494	75.6612824561
13	0.0194167279691	-0.00370326460032	-0.00173895405282	0.0229257437883	-0.00111923000957	0.0108846355714	-0.179364286371	0.0214165640478	-0.237095604279	-0.172549961895	-0.166046797026	-0.0397699856477	0.111559063997	-0.034067845431	6.62357706012E-5	1.63219934947	0.542572543726	0.674777925496	1.68296416317	0.398575131778	1.63200786457	-20.2604876775	7.32338830318	83.7286770118
14	0.457281539103	-0.411338881445	0.0536448987032	1.11816475802	-1.0175914553	1.26802274698	0.277948029403	0.415418094503	-0.8532103526	-0.310942048141	0.27153604955	-0.052207192014	0.602953061201	0.15294694764	1.16324886057	0.781387241213	-0.323354891254	0.0102479686048	0.567157830921	-0.347952691181	0.778381766324	-11.2550537162	-15.7292241007	23.6715620706

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 -2 through 17 )	A	A	-2 - 17
2	2	chain 'A' and (resid 18 through 67 )	A	A	18 - 67
3	3	chain 'A' and (resid 68 through 82 )	A	A	68 - 82
4	4	chain 'B' and (resid 3 through 163 )	B	B	3 - 163	1 - 161
5	5	chain 'B' and (resid 164 through 245 )	B	B	164 - 245	162 - 243
6	6	chain 'B' and (resid 246 through 445 )	B	B	246 - 445	244 - 443
7	7	chain 'B' and (resid 446 through 730 )	B	B	446 - 730	444 - 723
8	8	chain 'B' and (resid 731 through 1366 )	B	B	731 - 1366	724 - 1169
9	9	chain 'C' and (resid -7 through -3 )	C	C	-7 - -3
10	10	chain 'C' and (resid -2 through 2 )	C	C	-2 - 2
11	11	chain 'C' and (resid 3 through 12 )	C	C	3 - 12
12	12	chain 'C' and (resid 13 through 17 )	C	C	13 - 17
13	13	chain 'C' and (resid 18 through 20 )	C	C	18 - 20
14	14	chain 'D' and (resid -2 through 7 )	D	D	-2 - 7

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