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- PDB-7qqz: SpCas9 bound to FANCF off-target7 DNA substrate -

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Basic information

Entry
Database: PDB / ID: 7qqz
TitleSpCas9 bound to FANCF off-target7 DNA substrate
Components
  • (FANCF off-target7 ...) x 2
  • CRISPR-associated endonuclease Cas9/Csn1
  • FANCF 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 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. ...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 / 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: 2.25 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: FANCF sgRNA
B: CRISPR-associated endonuclease Cas9/Csn1
C: FANCF off-target7 target strand
D: FANCF off-target7 non-target strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,40317
Polymers197,9244
Non-polymers47913
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22890 Å2
ΔGint-179 kcal/mol
Surface area75890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.801, 66.686, 187.607
Angle α, β, γ (deg.)90.000, 110.830, 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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FANCF off-target7 ... , 2 types, 2 molecules CD

#3: DNA chain FANCF off-target7 target strand


Mass: 8604.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain FANCF off-target7 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

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Non-polymers , 3 types, 510 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.: 11 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.13 Å / Num. obs: 97227 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 54.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 7 % / Rmerge(I) obs: 1.82 / Mean I/σ(I) obs: 1 / Num. unique obs: 9668 / CC1/2: 0.484 / % possible all: 99.8

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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: 2.25→47.67 Å / SU ML: 0.3569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 4857 5 %
Rwork0.217 92302 -
obs0.2185 97159 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10910 2529 13 497 13949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002613932
X-RAY DIFFRACTIONf_angle_d0.497319308
X-RAY DIFFRACTIONf_chiral_restr0.03622201
X-RAY DIFFRACTIONf_plane_restr0.00282034
X-RAY DIFFRACTIONf_dihedral_angle_d17.5015650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.37821610.35543056X-RAY DIFFRACTION99.38
2.28-2.30.35941640.33263116X-RAY DIFFRACTION99.97
2.3-2.330.3451580.33193011X-RAY DIFFRACTION99.91
2.33-2.360.33891650.31623108X-RAY DIFFRACTION99.97
2.36-2.390.36851500.3133112X-RAY DIFFRACTION99.94
2.39-2.420.36811650.31433068X-RAY DIFFRACTION99.66
2.42-2.460.35771680.30423050X-RAY DIFFRACTION99.94
2.46-2.50.32111660.30183078X-RAY DIFFRACTION99.75
2.5-2.530.33691580.29693072X-RAY DIFFRACTION99.94
2.53-2.580.33281630.2873108X-RAY DIFFRACTION99.85
2.58-2.620.32421710.29123048X-RAY DIFFRACTION99.63
2.62-2.670.32281620.28863053X-RAY DIFFRACTION99.01
2.67-2.720.35371530.2963070X-RAY DIFFRACTION99.35
2.72-2.770.3661570.30673094X-RAY DIFFRACTION99.36
2.77-2.830.34661700.30443016X-RAY DIFFRACTION99.47
2.83-2.90.35141660.28323126X-RAY DIFFRACTION99.34
2.9-2.970.33331620.29063028X-RAY DIFFRACTION98.7
2.97-3.050.29981610.28913060X-RAY DIFFRACTION98.56
3.05-3.140.30921550.28632993X-RAY DIFFRACTION97.31
3.14-3.240.32351520.2762937X-RAY DIFFRACTION94.75
3.24-3.360.31561540.26053082X-RAY DIFFRACTION99.45
3.36-3.50.26681710.24323102X-RAY DIFFRACTION99.63
3.5-3.650.25921620.22333101X-RAY DIFFRACTION99.79
3.65-3.850.22451610.20523105X-RAY DIFFRACTION99.63
3.85-4.090.20071650.17463081X-RAY DIFFRACTION99.45
4.09-4.40.18431610.16553104X-RAY DIFFRACTION99.51
4.4-4.850.20241640.15933123X-RAY DIFFRACTION99.34
4.85-5.550.17161660.15513107X-RAY DIFFRACTION97.91
5.55-6.980.20491570.17423044X-RAY DIFFRACTION96.94
6.98-47.670.17111690.1543249X-RAY DIFFRACTION99.45
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)
10.235900368391-0.37156440691-0.3617960510380.3525948988620.6816132823152.37766275059-0.1761130626420.0258311595303-0.03265443847420.223413157960.06474769074150.04487427164760.950519002441-0.259552570220.1723259555030.66610257213-0.1079772122070.07792778748950.581267013189-0.04152813792440.555180352045-6.968692738716.9385780555361.1865085342
21.33911321007-0.6783873497710.02228599285840.948302530505-0.4803197664530.862931961460.426650144930.621958017566-0.217766068643-0.188580459032-0.09767235376-0.2580960649720.6378233495170.145345570278-0.3680076445830.6173929941180.0892416480835-0.0008487589115730.762150848333-0.1359728271490.55485872858418.3944078748-5.4545906768813.331178074
34.706079275481.131124472612.532231625680.9342148947411.164882658594.205314799980.4265588035040.1176202136770.0641859186301-0.510986953319-0.09796524981310.580786189770.209632014418-0.821762840879-0.1892793182811.341245885140.139781050968-0.2520315582941.24929855486-0.2222508779691.1247007219219.0867449947-19.85061755553.55914253141
41.166152216750.6775548194880.3456479244610.521977441972-0.1855623137560.7027499051940.06591384587640.1021845222270.124991280577-0.04712836418-0.005018839961310.0576717974109-0.02924890485420.0383903266563-0.03649187408850.471775645083-0.0636734260883-0.03368476925190.4728796551170.004825129209230.453207112495-0.7739064896178.7325654793929.1162525462
50.006826299748-0.076173383673-0.03001605003360.7633163808550.3506726772970.1614522178750.3913920955230.2815691106051.249638420.0318361018561-0.128774322931-0.155141410982-2.184765579970.877344376462-0.3270704501421.36298380709-0.169276214250.1813538048070.9449975286750.2322105354141.38157917323-38.616043992217.28789249729.2619386794
63.43658093399-0.4170052191510.04660606595783.631350969550.6520689214294.116265654910.504737102507-0.3043080660460.185548984865-0.1500726999410.0662225545308-0.504365784305-1.645186646291.12347022628-0.6077540827940.996996115515-0.3390659447840.1798395908171.08513805879-0.02287087483390.938054127687-39.643454697714.535508859537.3070141627
70.6854271802510.1982594422140.008109795931470.251830098768-0.148496845910.553568952950.09113161279960.00833032256577-0.006158480603810.0520863893055-0.0887963663004-0.0474492603303-0.02251054797220.1462472847330.01229804668950.462732244188-0.0519156535597-0.01158003426850.417084867928-0.02285260714850.4495209177986.065305797656.4781522531537.4121799791
80.890412484645-0.1111362432970.9883396957440.436845475303-0.6242235088533.21868421485-0.0738605438984-0.08714906613190.02594556470280.214305107566-0.1062745055250.0740743527163-0.22093253524-0.1523162617280.1939183520650.6337378235170.0404330984209-0.005526891524530.586385021843-0.01086160571090.65299718645626.4609038349-3.5782393651556.5415406464
91.49754637257-0.0603596057682-0.2921531388520.5495475508080.3429562308861.386227207730.0976361719678-0.0772919387249-0.1272856869440.150554684382-0.01126760790470.007735848084580.08723927311870.200356086357-0.07303635650030.484138938331-0.0435158075001-0.04971363309360.4977443796440.05223512559090.4631803346216.22578497775.9225767062137.581756004
101.244465526380.183562721278-0.5382988308981.02629034355-0.7668114994222.29421440442-0.0937084742251-0.0008200741933510.02376251996940.02149049121010.0447655667368-0.108358233551-0.002200916946420.06183684660130.03813026764730.45744297383-0.00266772075955-0.02445996325090.368703624647-0.04114604894320.4833184584120.86023443234118.979798852180.6058917265
110.319665394481-0.07929088054850.2005132143930.181628086563-0.2429280008750.4397771214660.07661169985790.0115747222098-0.134883742192-0.00380749841195-0.0327985162088-0.06123274467440.1865140180890.00129376526302-0.04205821370720.56305746493-0.02087814760230.01024276790470.562491717549-0.01929702801130.637891289677-10.0141414983-6.0580305619166.360653825
120.8907441525140.198593512854-0.4579627669050.372402166994-0.1793554003691.34696590714-0.09856496681850.0311756931097-0.167525034906-0.01396966139310.05599960888880.03187998842190.375925213147-0.1775696804590.0308887356280.517030875515-0.0978650408150.005016548227580.444886513376-0.01306672945330.519078701543-29.1344548919-11.842723697143.6687665429
135.082986512612.378940774730.8400855681041.904393951421.918846695923.120704487250.1708399699340.988135653727-0.560260942185-0.206592965846-0.3068492027110.565614031036-0.172894914545-1.35967090820.2308067635531.11426533072-0.4201010809710.1089572732421.96037258241-0.5046831544351.03424846668-16.0999434417-19.813638574218.4573524753
140.391389011518-0.0972344503771-0.1150351472130.0337509634776-0.06490252852870.16584202010.023134398895-0.115155547151-0.130356023623-0.02020243212340.01721556084670.09229539610680.07636917844950.08356837810790.03659524653630.55295498772-0.05707268542810.05232977491620.6057797235720.004744383755680.530722028374-1.340241595381.6045857228247.2489563301
150.162188250714-0.0438793047633-0.06757429782690.1521348841370.4607432771162.68373836083-0.1371268239510.321545201763-0.175592998369-0.2893931417990.146443274720.2380233135290.461566407712-0.255865490375-0.1484639754810.799908183121-0.1351608829090.02809675843170.6477533114-0.03196979736230.614002697418-14.33511111873.0407273472178.2154260098
164.49440158764-0.627486854678-2.324661611744.48030452440.2623012845354.69275971571-0.1454131601470.596873976701-1.06672635784-0.146140487958-0.01068062132-0.2492006095971.04890929365-0.0188423396748-0.121135722730.697229596036-0.118157373444-0.04800710185680.637274966004-0.1481129708520.82925115327-11.5426953194-14.081432795223.3605873137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 74 )
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 82 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 207 )
8X-RAY DIFFRACTION8chain 'B' and (resid 208 through 342 )
9X-RAY DIFFRACTION9chain 'B' and (resid 343 through 493 )
10X-RAY DIFFRACTION10chain 'B' and (resid 494 through 678 )
11X-RAY DIFFRACTION11chain 'B' and (resid 679 through 905 )
12X-RAY DIFFRACTION12chain 'B' and (resid 906 through 1366 )
13X-RAY DIFFRACTION13chain 'C' and (resid -7 through -3 )
14X-RAY DIFFRACTION14chain 'C' and (resid -2 through 12 )
15X-RAY DIFFRACTION15chain 'C' and (resid 13 through 20 )
16X-RAY DIFFRACTION16chain 'D' and (resid -2 through 7 )

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