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- PDB-7ox9: Target-bound SpCas9 complex with AAVS1 all-RNA guide -

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Basic information

Entry
Database: PDB / ID: 7ox9
TitleTarget-bound SpCas9 complex with AAVS1 all-RNA guide
Components
  • AAVS1 non-target DNA strand
  • AAVS1 target DNA strand
  • CRISPR-associated endonuclease Cas9/Csn1
  • sgRNASubgenomic mRNA
KeywordsHYDROLASE / Cas9 / CRISPR / sgRNA / AAVS1 / nuclease
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 serotype M1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPacesa, M. / Donohoue, P. / May, A.P. / Jinek, M. / Cameron, P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182567 Switzerland
CitationJournal: Mol.Cell / Year: 2021
Title: Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Authors: Donohoue, P.D. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.S. / Gibson, J. / Kohrs, B. / Baek, K. / Owen, A.L.G. / Slorach, E.M. / van ...Authors: Donohoue, P.D. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.S. / Gibson, J. / Kohrs, B. / Baek, K. / Owen, A.L.G. / Slorach, E.M. / van Overbeek, M. / Fuller, C.K. / May, A.P. / Jinek, M. / Cameron, P.
History
DepositionJun 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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: sgRNA
B: CRISPR-associated endonuclease Cas9/Csn1
C: AAVS1 target DNA strand
D: AAVS1 non-target DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,83917
Polymers198,3604
Non-polymers47913
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22770 Å2
ΔGint-175 kcal/mol
Surface area76910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.080, 68.205, 187.771
Angle α, β, γ (deg.)90.000, 111.144, 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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DNA chain , 2 types, 2 molecules CD

#3: DNA chain AAVS1 target DNA strand


Mass: 8446.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain AAVS1 non-target DNA strand


Mass: 3748.449 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 sgRNA / Subgenomic mRNA


Mass: 27290.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9


Mass: 158875.031 Da / Num. of mol.: 1 / Mutation: D10A, H840A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: cas9, csn1, SPy_1046 / Plasmid: pMJ841 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 500 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 / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
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: Oct 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→48.16 Å / Num. obs: 77217 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 53.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.606 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 7600 / CC1/2: 0.493 / % possible all: 98.69

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Processing

Software
NameVersionClassification
Coot0.8.9model building
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ5
Resolution: 2.45→48.16 Å / SU ML: 0.3871 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 3863 5.01 %
Rwork0.1948 73317 -
obs0.1968 77180 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.89 Å2
Refinement stepCycle: LAST / Resolution: 2.45→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10930 2540 13 487 13970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003313966
X-RAY DIFFRACTIONf_angle_d0.625919360
X-RAY DIFFRACTIONf_chiral_restr0.03942206
X-RAY DIFFRACTIONf_plane_restr0.0042037
X-RAY DIFFRACTIONf_dihedral_angle_d18.78525661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.37581450.36382535X-RAY DIFFRACTION98.53
2.48-2.510.31621260.32922639X-RAY DIFFRACTION98.75
2.51-2.540.37751380.32172532X-RAY DIFFRACTION98.67
2.54-2.580.33751320.29972599X-RAY DIFFRACTION97.71
2.58-2.620.34291410.28642590X-RAY DIFFRACTION99.6
2.62-2.660.3431360.28592608X-RAY DIFFRACTION99.6
2.66-2.70.31381370.27412610X-RAY DIFFRACTION99.67
2.7-2.740.3871380.26732610X-RAY DIFFRACTION99.85
2.74-2.790.29311440.25832627X-RAY DIFFRACTION99.93
2.79-2.840.30631310.25282637X-RAY DIFFRACTION99.93
2.84-2.890.28061390.24362607X-RAY DIFFRACTION99.89
2.89-2.950.3111410.25442624X-RAY DIFFRACTION99.82
2.95-3.020.30161360.25482600X-RAY DIFFRACTION99.71
3.02-3.090.2871380.25182654X-RAY DIFFRACTION99.79
3.09-3.160.2591380.22922609X-RAY DIFFRACTION99.64
3.16-3.250.26231390.21552598X-RAY DIFFRACTION99.35
3.25-3.340.26671360.20132601X-RAY DIFFRACTION99.24
3.35-3.450.26141350.2012626X-RAY DIFFRACTION99.07
3.45-3.580.25621400.19452614X-RAY DIFFRACTION98.89
3.58-3.720.24341350.18772551X-RAY DIFFRACTION97.6
3.72-3.890.18881390.17262608X-RAY DIFFRACTION99.21
3.89-4.090.18281380.16182661X-RAY DIFFRACTION99.64
4.09-4.350.19871390.15292636X-RAY DIFFRACTION99.36
4.35-4.690.17791370.13932630X-RAY DIFFRACTION99.64
4.69-5.160.18211420.14592651X-RAY DIFFRACTION99.68
5.16-5.90.20751410.16352673X-RAY DIFFRACTION99.43
5.9-7.430.21051380.18132632X-RAY DIFFRACTION97.67
7.43-48.160.17221440.1652755X-RAY DIFFRACTION99.31
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)
10.638690624628-0.449303575450.4204012661010.3557209913390.2458124304852.66303810815-0.223423405681-0.1052178614010.03747685605970.05735842814620.1609937944860.1253087557140.718754823835-0.547898941170.05671116390810.508582848694-0.07980806199170.06789139680060.407091103879-0.05035764669770.508371302166-7.144867215036.3658845160961.0229265621
20.844755908461-0.1035693557860.1664029373231.185216155420.499738068530.7255883649020.3415230958950.7427876350550.0870122414149-0.2029876199020.187117098301-0.3351093530961.033223009770.444349100757-0.04740207156570.7001083237670.192586533393-0.07467329125550.898772047404-0.1644012234690.43509109172118.3055093016-5.5036681461813.340983642
33.279421477240.4251500235120.4347990972181.837210563750.04917736048642.857125523960.5414039166150.844178427788-0.0752343433185-0.93467743010.0003259974730690.6484644105280.4594945354640.119663728745-0.471411622621.423163946070.273550170377-0.2746922615561.3339348841-0.2941099992090.98987307235219.3310277531-19.77693133553.16173784678
41.37429570670.4957147692720.5894663153670.4900941400820.09678027097491.474863176920.08139226406050.1745748013310.099979737361-0.119107324358-0.02574940023670.074745088244-0.03632212185040.168573423889-0.1284745932640.354708042859-0.0244147330913-0.02204264370940.3383597606660.01067991670230.34437510837-1.049691803528.5686658621329.1730566877
50.206872539434-0.422337320716-0.0220768364941.055067305410.6928973279282.098749738530.657366077259-0.2300792901561.58763951439-0.214682778612-0.0420961890967-0.40894741244-2.037995816511.08540958457-0.3158884057131.20395510931-0.2213858157280.2412164101860.8280645331370.2360390314111.44989302946-38.829359331516.916540171929.4190263984
62.936676074032.19784256622-0.9928003067542.99408456995-1.214662083460.8933597612790.470358732186-1.011913901580.349326679283-0.0413775647756-0.0407874116227-0.109569802984-1.467663595020.506677679585-0.3029996352661.09957299251-0.2615699235740.2049857273381.28487108665-0.1389065099410.852861664638-39.916579062514.210313754637.4150948197
70.3747105815930.08768486658120.221211969930.280490442433-0.02171762985931.156834459920.09030780240170.121208494588-0.08781895883830.139782781885-0.0527291989981-0.1086742658190.1667020002130.492716781096-0.04963807266170.4456393933360.0281978293737-0.04096456555250.485877590679-0.03736935601150.4635714120915.393505856-0.54604362983742.5212916845
80.499483555120.06808227087680.09031639334110.314456799469-0.06562816912282.43193910543-0.088410159024-0.1181552726750.036918559950.203123925010.0733119046714-0.0487223819423-0.4033906589890.01595918602490.05199497994870.5368755843780.0382506224002-0.01245158904360.250208744742-0.01906320350020.4314844164590.37854859601920.368907889469.4033933021
90.669645052706-0.9204118452070.4978869628261.20772734504-0.4890776836621.49322194510.111641194238-0.00533722418605-0.07269518175780.0102374150088-0.0653074853331-0.2450208678610.498217295290.249249776554-0.1025340421890.569699637826-0.0304018568702-0.004953438208980.44442998287-0.03657400564890.62119221008-7.51739862944-14.793461882364.1443750328
101.270903955860.200676516031-0.3367286441780.375722146264-0.08410306442571.5059534725-0.09793016413710.0266025045912-0.2025645565240.05173486815320.0683333743650.04133182842890.461595834932-0.2943159930930.0165085410980.512975338754-0.1351791397830.0287208211170.406644824291-0.02948386591630.498853326744-29.4285980528-12.488223099343.6707900948
110.87600386827-0.0266096175905-0.1711969849310.200690587449-0.6642645519962.265225137090.2479334688750.250370726657-0.877981974745-0.286834967050.2315748956970.3159762135050.476658984865-1.196666418450.0568904359561.32202681244-0.676081475362-0.07027886919071.78792923073-0.4520041336010.988285100177-15.765087749-21.32226327919.0168749386
122.033991833170.9558426298870.05316050334491.18427670947-0.5093017669310.39558247983-0.0171920171593-0.45873935298-0.4256066070240.220875916470.0203199335457-0.1622916952770.2079299716010.340114541619-0.01392973813020.505312972803-0.108437814734-0.01253297166220.477172019478-0.1068930898580.544706094367-2.58909014998-9.6729087706231.1845158845
132.428361517280.0918102945678-0.8709894766360.658965173313-0.4799102814891.57852437230.21163832908-0.03774362211940.3219454730580.346007646280.0964080776131-0.04730752483010.181790032741-0.231648816506-0.343565108660.5022371212-0.1087969989660.001369174225620.3847258936220.02966486655020.395390725532-1.007962270266.9227630228155.0741740008
141.22442471009-0.258451809911-0.03159834231670.703670853245-0.07934777491212.13501378421-0.263253785159-0.13103567028-0.1437652602060.2494364278560.2137953216710.4987981838340.724046209967-0.956774356138-0.1008049037370.686301967799-0.04121016921440.09073487566970.6494042136410.0638314503070.560459361831-14.57896015332.6156878086378.0958930291
154.23518910798-0.0106545441336-0.9942298204635.988548705130.5856174840712.69683283563-0.03775859117450.441272736575-1.048187989140.182971829661-0.0553417492978-0.006630176233531.194415780140.114042717256-0.02090061307830.617597888528-0.0743033980408-0.00154868329770.493309798249-0.1771353652950.695358553239-11.6585352783-14.624622538424.0642525731
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 411 )
8X-RAY DIFFRACTION8chain 'B' and (resid 412 through 730 )
9X-RAY DIFFRACTION9chain 'B' and (resid 731 through 905 )
10X-RAY DIFFRACTION10chain 'B' and (resid 906 through 1367 )
11X-RAY DIFFRACTION11chain 'C' and (resid -7 through -3 )
12X-RAY DIFFRACTION12chain 'C' and (resid -2 through 2 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 12 )
14X-RAY DIFFRACTION14chain 'C' and (resid 13 through 20 )
15X-RAY DIFFRACTION15chain 'D' and (resid -2 through 7 )

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