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- PDB-7qr0: SpCas9 bound to TRAC off-target1 DNA substrate -

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Basic information

Entry
Database: PDB / ID: 7qr0
TitleSpCas9 bound to TRAC off-target1 DNA substrate
Components
  • (TRAC off-target1 ...) x 2
  • CRISPR-associated endonuclease Cas9/Csn1
  • TRAC sgRNA
KeywordsHYDROLASE / 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
CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, bridge helix / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / Bridge helix of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / Cas9 RuvC domain / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain ...CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, bridge helix / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / Bridge helix of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / Cas9 RuvC domain / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9/Csn1
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPacesa, M. / Jinek, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182567 Switzerland
CitationJournal: 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
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAC sgRNA
B: CRISPR-associated endonuclease Cas9/Csn1
C: TRAC off-target1 target strand
D: TRAC off-target1 non-target strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,71723
Polymers198,0044
Non-polymers71319
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23800 Å2
ΔGint-183 kcal/mol
Surface area75730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.547, 67.421, 187.247
Angle α, β, γ (deg.)90.000, 111.488, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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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Components

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TRAC off-target1 ... , 2 types, 2 molecules CD

#3: DNA chain TRAC off-target1 target strand


Mass: 8589.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain TRAC off-target1 non-target strand


Mass: 3692.426 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 TRAC sgRNA


Mass: 27133.156 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, 677 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.: 17 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.13 Å / Num. obs: 92030 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 49.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.91 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9144 / CC1/2: 0.339 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ5
Resolution: 2.3→47.71 Å / SU ML: 0.3307 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 4601 5 %
Rwork0.1939 87397 -
obs0.1954 91998 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10891 2500 19 658 14068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001813881
X-RAY DIFFRACTIONf_angle_d0.450419234
X-RAY DIFFRACTIONf_chiral_restr0.03472194
X-RAY DIFFRACTIONf_plane_restr0.00272027
X-RAY DIFFRACTIONf_dihedral_angle_d17.8595627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.32181550.33292949X-RAY DIFFRACTION99.81
2.33-2.350.36551510.32182857X-RAY DIFFRACTION99.97
2.35-2.380.37321490.32822880X-RAY DIFFRACTION100
2.38-2.410.34291560.31642917X-RAY DIFFRACTION99.87
2.41-2.440.35641550.30562864X-RAY DIFFRACTION99.93
2.44-2.480.33611520.30232872X-RAY DIFFRACTION99.97
2.48-2.510.34031470.29312914X-RAY DIFFRACTION99.9
2.51-2.550.33731520.28762868X-RAY DIFFRACTION99.97
2.55-2.590.33161570.28172925X-RAY DIFFRACTION100
2.59-2.630.31861550.26692904X-RAY DIFFRACTION99.97
2.63-2.680.28361520.2562874X-RAY DIFFRACTION99.97
2.68-2.730.31721470.25992898X-RAY DIFFRACTION99.97
2.73-2.780.28211520.25912921X-RAY DIFFRACTION100
2.78-2.840.30311570.25252865X-RAY DIFFRACTION99.97
2.84-2.90.3091520.24772928X-RAY DIFFRACTION99.97
2.9-2.970.28341510.24172928X-RAY DIFFRACTION100
2.97-3.040.27041520.24132888X-RAY DIFFRACTION100
3.04-3.120.28291520.22532894X-RAY DIFFRACTION99.97
3.12-3.210.25811580.21482927X-RAY DIFFRACTION100
3.21-3.320.22971530.20032898X-RAY DIFFRACTION99.97
3.32-3.440.24811470.18962918X-RAY DIFFRACTION99.84
3.44-3.570.19631560.18542891X-RAY DIFFRACTION99.87
3.57-3.740.2011550.17872939X-RAY DIFFRACTION99.81
3.74-3.930.1711500.15812912X-RAY DIFFRACTION99.97
3.93-4.180.17141570.14852921X-RAY DIFFRACTION100
4.18-4.50.14821530.14152966X-RAY DIFFRACTION100
4.5-4.950.16181580.13832918X-RAY DIFFRACTION100
4.95-5.670.20481550.14862950X-RAY DIFFRACTION99.84
5.67-7.140.19621550.17712959X-RAY DIFFRACTION99.74
7.14-47.710.18231600.16163052X-RAY DIFFRACTION99.35
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1679884256950.3246539675990.4277503346571.541215775582.381070362593.7115080090.1371556290580.02923345679760.3413668468570.4084826827130.03535245129680.4241380277060.468728975974-0.433847194769-0.2038899178560.607352935901-0.1021446129460.0470267409110.6146661332470.02333095320060.539454855823-15.13684274923.3450516518177.8074041586
24.56934832613-0.690431763821-0.9458732700855.357186851870.6112844425244.319361227130.3562947328040.532203576158-1.01774552696-0.1795965989120.206738418047-0.3229342357820.9105381292430.385042112516-0.4011244359120.522636503836-0.0492035326573-0.02530869286480.431743571414-0.2121691637840.660180947315-11.5446072271-14.479682027724.0948454575
31.0234840735-1.29743610367-0.2690704237425.278259166362.948210486526.66391735621-0.1256353777570.0567585575821-0.2600718183010.0654983872673-0.2983411400030.7456807025990.259194844978-0.7070163313830.4574686958740.572958069705-0.1385322390470.04828658088330.599698974406-0.103986793910.544582346574-10.73768600415.8872728763671.5959496155
41.43363681029-0.168805535227-0.1888336607260.8492602063030.6700607226031.56723610470.04878820210660.04708668343140.006810837298810.159460897350.129283789746-0.06592182358080.3701538645910.340691394701-0.05081904831170.4292953192080.03502289699470.002040686881440.428220426813-0.008111566033240.3959191471778.381679744653.3294944778231.5891259903
50.1102652000680.005930827427040.5454641891260.2247750889140.1591705528642.988130378080.4241273000820.582577948246-0.0336271733631-0.9968963118570.07240773929080.5217442536220.5046738333230.160265674972-0.3073165565231.345717674460.235308353524-0.1513864359761.54277762237-0.2068612917170.84578174900422.5471208935-18.10405711631.72837960777
60.9552563469130.1677523112660.5177719559660.711777533665-0.08551402139311.263467689020.00846987655020.2108841927450.148093109853-0.05121434986240.0187659559930.07992244210320.004461458723890.116478737165-0.06476846006410.339377949453-0.0412642188658-0.020120214510.3628108532490.007113622956670.35359605598-3.227437659069.7476392392129.4045848351
70.03342818121540.240149090021-0.001455043919791.90942539107-0.06615550492110.0464118142334-0.00323654517130.06987617751870.489185073182-0.760756239351-0.0126606672715-0.734868261828-1.842247223991.15190625844-0.1405823106431.59512677514-0.3827879277610.3791248763161.130345315670.2226042097021.46757570476-37.465190753619.919322788329.3069209986
83.56959764002-0.8567073605130.3242252428794.207509193240.7404731796685.344966273340.177575727667-0.3641371882970.23379027349-0.517377224536-0.00425039663593-0.630623592503-1.551492609590.650338398644-0.1209129878860.796896729495-0.1975090389630.1201197095611.00635864326-0.02936629930140.8761764187-41.179101765213.630075266537.7704504959
90.9829424488870.3622669936640.01542334224990.367569930194-0.1956640853220.8999501035820.09373466256760.1071354517860.05021300697010.0604030035664-0.0656772944736-0.013975406575-0.02104466217210.249001210084-0.02698658605770.354732221235-0.03903244701910.01083863954640.367331449398-0.04436478216030.3563695027955.347923187896.6082454133837.1133095924
102.29503997182-0.8114260671180.3919425632431.98009244686-0.820223369093.258055764320.1371918458750.347677212267-0.333407746946-0.0758969398116-0.2665269178350.582530543006-0.822467119558-1.207770264010.02931833848490.8079220507940.215992094566-0.04301792112820.804319028787-0.1048477833490.72615281468223.2017744886-3.7628892142366.4596382826
110.458868435939-0.143210194571-0.0936130133990.2365193145940.1492663570641.787665509610.005800689379590.00307178624310.004021549668060.0957480263060.0744553018571-0.05899959246940.02015375049590.302740083675-0.06689670339190.36393246053-0.0236511148728-0.03687960301660.342679102595-0.003710444266780.42378074860510.257448216611.078076847258.3560098293
120.2329996318370.05153595958550.1721793890250.297458032720.05006275767170.8836008119-0.0142903581928-0.0694464563877-0.1129791542410.1109500678880.0831384193777-0.03565994659530.1967295648640.0303350228145-0.04280764022270.5195640951520.01842447009680.02620092901350.495920206679-0.005440486808880.540608607927-10.7539250799-6.2528058904166.2980325549
131.311186007490.153987307168-0.3695305536390.461862960344-0.01924106986841.40302265957-0.1005163275080.0760268680113-0.2083983254360.04288972683350.08286613311280.04115322050080.437964550001-0.2573187591480.007950284784380.436216341237-0.1128589511880.005071677119720.315752462713-0.01526811031510.436731860467-29.7481324458-11.740888312642.9360136477
140.852351074230.809325575510.5020980816081.287521843150.4297114277291.429043645610.1770329434260.167803866318-0.4881200814760.145129000366-0.06305026085750.05465109269430.0472813817101-0.786629591782-0.0549859312741.11451001057-0.337858301576-0.04948782622081.56922587338-0.50751252161.01066916459-15.7910946824-21.792304339519.2358468947
152.531599009331.47355426236-0.1295876431932.60377395445-0.5484527847550.8524122826390.284860201747-0.0421232140308-0.400192405252-0.0313864338794-0.3802593273660.2252662121020.4839644216420.2711412732450.00794550052610.4921286859820.0253157614716-0.04240496161170.391037955175-0.04029318369570.429652961777-2.69251639038-9.1818934195931.1100943264
163.13446794975-1.64032897502-0.7898692658343.657350866572.40173071444.01638061190.07083660553840.3478884814150.1403839718940.7191537351470.41840163747-0.3605092337840.914036931716-0.204262309342-0.3673483929720.562366104186-0.102487455524-0.03783402793180.449270371003-0.001372217389190.4207153043015.913017048014.0653398962848.7869858683
170.523893052573-0.496924660829-0.837606558242.40860976881-0.5135584847182.238442832330.1324750734130.110723689550.3624394207550.448894623980.112875706740.541618688180.0677774761192-0.314451186071-0.2313196544930.503092380643-0.06113773425930.1127415067080.4539269061610.03096734661170.49816600854-8.5665102742310.182139839560.3583153251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 13 through 20 )
2X-RAY DIFFRACTION2chain 'D' and (resid -3 through 7 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 10 )
4X-RAY DIFFRACTION4chain 'A' and (resid 11 through 30 )
5X-RAY DIFFRACTION5chain 'A' and (resid 31 through 40 )
6X-RAY DIFFRACTION6chain 'A' and (resid 41 through 70 )
7X-RAY DIFFRACTION7chain 'A' and (resid 71 through 75 )
8X-RAY DIFFRACTION8chain 'A' and (resid 76 through 82 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 207 )
10X-RAY DIFFRACTION10chain 'B' and (resid 208 through 284 )
11X-RAY DIFFRACTION11chain 'B' and (resid 285 through 678 )
12X-RAY DIFFRACTION12chain 'B' and (resid 679 through 909 )
13X-RAY DIFFRACTION13chain 'B' and (resid 910 through 1367 )
14X-RAY DIFFRACTION14chain 'C' and (resid -7 through -3 )
15X-RAY DIFFRACTION15chain 'C' and (resid -2 through 2 )
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 7 )
17X-RAY DIFFRACTION17chain 'C' and (resid 8 through 12 )

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