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- PDB-7qr8: SpCas9 bound to PTPRC off-target1 DNA substrate -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7qr8
TitleSpCas9 bound to PTPRC off-target1 DNA substrate
Components
  • (PTPRC off-target1 ...) x 2
  • CRISPR-associated endonuclease Cas9/Csn1
  • PTPRC 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: 2.75 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: PTPRC sgRNA
B: CRISPR-associated endonuclease Cas9/Csn1
C: PTPRC off-target1 target strand
D: PTPRC off-target1 non-target strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,72916
Polymers198,2894
Non-polymers44012
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22100 Å2
ΔGint-185 kcal/mol
Surface area76900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.278, 68.029, 186.741
Angle α, β, γ (deg.)90.000, 110.740, 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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PTPRC off-target1 ... , 2 types, 2 molecules CD

#3: DNA chain PTPRC off-target1 target strand


Mass: 8707.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain PTPRC off-target1 non-target strand


Mass: 3629.365 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 PTPRC sgRNA


Mass: 27363.361 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, 203 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.: 191 / 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: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→48.12 Å / Num. obs: 54916 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 58.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.5
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 1 / Num. unique obs: 5429 / CC1/2: 0.544

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ5
Resolution: 2.75→48.12 Å / SU ML: 0.4046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2502 2741 4.99 %
Rwork0.2215 52147 -
obs0.2229 54888 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.35 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10883 2558 12 191 13644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003813938
X-RAY DIFFRACTIONf_angle_d0.622819327
X-RAY DIFFRACTIONf_chiral_restr0.04472205
X-RAY DIFFRACTIONf_plane_restr0.00332030
X-RAY DIFFRACTIONf_dihedral_angle_d15.4915651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80.41741370.36672590X-RAY DIFFRACTION99.93
2.8-2.850.35751300.35542571X-RAY DIFFRACTION99.96
2.85-2.90.37661370.34182566X-RAY DIFFRACTION99.89
2.9-2.960.34751350.31992632X-RAY DIFFRACTION99.93
2.96-3.030.34991400.32062548X-RAY DIFFRACTION99.96
3.03-3.10.36291330.32162629X-RAY DIFFRACTION99.93
3.1-3.170.30941390.31832555X-RAY DIFFRACTION100
3.17-3.260.26671400.27392594X-RAY DIFFRACTION99.89
3.26-3.360.26041310.24922581X-RAY DIFFRACTION99.89
3.36-3.460.29431320.23972609X-RAY DIFFRACTION99.96
3.46-3.590.24631410.23632605X-RAY DIFFRACTION99.89
3.59-3.730.2771390.22572580X-RAY DIFFRACTION99.93
3.73-3.90.24571330.20722608X-RAY DIFFRACTION100
3.9-4.110.19251400.19292603X-RAY DIFFRACTION100
4.11-4.360.19531360.18522623X-RAY DIFFRACTION99.96
4.36-4.70.21661390.17432605X-RAY DIFFRACTION99.96
4.7-5.170.22471370.17632621X-RAY DIFFRACTION99.96
5.17-5.920.24411380.19252649X-RAY DIFFRACTION100
5.92-7.460.22561410.20932656X-RAY DIFFRACTION99.96
7.46-48.120.20891430.17542722X-RAY DIFFRACTION99.55
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)
12.734897684790.6910367931060.05934222544793.06639945107-0.06119455759972.45347371104-0.3771253881770.243996381907-0.6198165874050.415444097210.161818709560.9682988522091.98775742843-1.542948440980.317878238711.14429051321-0.3074937326240.3257744124211.15206480597-0.2774751274281.07185466501-16.11890944674.8349254298474.8883405368
22.83792018816-0.735429783745-0.9669964431451.459757084310.5128395798151.702009735810.0652696933341-0.533818672889-0.3612236318350.7254847458660.269326621116-0.117872829690.31274126840.507506925708-0.343349061140.717105996218-0.02476175457610.005647910957650.476739627702-0.02405166675140.579926037635-3.304888952816.2899242876951.1854174761
31.33342407216-0.1627989490170.28511509981.339456674530.2811439200821.239739153350.218035420280.5893474480550.2245153498750.187895198645-0.0125973528234-0.2494855350940.3525666688110.0991914352185-0.2870906463990.4212096391010.00698388389174-0.01428166122180.577848846678-0.01287237948520.48445459547513.28630101530.099765709464423.4218307052
41.04001999533-0.335958982547-0.6661573537551.856017348230.8634427523611.309731082930.2158452408190.480169597081-0.00157292120149-0.827008650597-0.15671955775-0.324363659480.2768381449590.156672699249-0.07121706990671.232034667190.393127905195-0.03226824382411.22407449806-0.2378609664910.75466576218926.1275880995-13.23270603623.99738835188
50.90561859596-0.09271143545640.3630789679010.913543340595-0.1244085700272.327265137050.1832026798120.536538420889-0.594789293476-1.4511479317-0.2347210590740.5007725899190.677205571797-0.5054615157530.1646499484191.377022238630.198809614887-0.201930011.13172613131-0.2434311284270.79750047683821.9776422482-17.12877139318.03498183349
60.4682747433770.546369115472-0.2902480657561.087365335460.3558030478061.32799114044-0.005509523652630.268688816705-0.02637492658080.132517720498-0.116093349383-0.176135299577-0.01885335376030.1069798242850.09244896467430.40477995056-0.000615851477701-0.04848962092530.598615479777-0.05356347987080.39203505113917.07950700093.2121809796525.7370446415
73.35823288552-0.05154363094940.6440050476240.800529041309-0.3164493580861.83254831846-0.01288471933820.216135931816-0.416682394946-0.2482660951730.08369321283880.246471490194-0.269769233158-0.0200457153478-0.09373582560390.397273925307-0.0059892783182-0.02451222039710.3702816172020.01632245099480.428780368954-2.044659082959.5632753607826.8417033039
81.433010634210.3789324864661.259756975380.0912987041110.3317238371681.10112042392-0.171199533805-0.2324562497210.8965075774430.00843770137386-0.15725012947-0.415708872302-0.613541021316-0.2519541929710.304131140810.80821590331-0.022381884435-0.0944999799360.4093172831460.02541565126910.801902479848-7.5926497103424.171672606228.9453588077
92.401745445912.01064712206-0.231279312731.71717361548-0.2213628414010.336105643014-0.00158206157301-0.1596461782390.68437090492-0.416851610857-0.014688991564-0.0563364776242-0.611586221598-0.1127099445680.09916759140920.459416056432-0.01025850342720.0231514206120.2690160805550.04219090500440.509620058298-4.8845316373516.290174389735.308452653
101.15361047884-1.16252084156-1.010885539871.94183581708-0.1520312560462.58698440672-0.1297806089640.461490575984-0.07570922038440.0393265737829-0.367265481807-0.317005662479-0.437296064788-0.2537429290670.4771666138770.456793760004-0.124022101008-0.001335134814240.479797922089-0.02293742883170.567189363214-24.42514569415.5677685215239.3988835737
112.770962281520.6419184139770.5881457350720.2763583569840.9172391947494.93551317634-0.0732083339728-0.003658371126711.79484876987-0.1211084782630.01767352442040.366387829766-1.953044895720.3656503525380.2645991061560.948733773271-0.186923029340.001120668799970.7042703360910.2148605356341.32271520642-40.02985323712.686016151329.954203816
124.012989967820.214258589295-1.06117679122.19874060503-1.018561861144.56239160521-0.140470915678-0.2164183059620.118303985817-0.7714954619480.236963933975-0.749663290826-2.108079034780.645296024779-0.2292825498951.24431622632-0.3340890000930.1277897921091.17364603178-0.003325776021871.08253295608-39.212303323315.103339252936.3067237476
131.466247851660.1477426358990.08301606334760.286216115014-0.1341031098761.185884009020.0979120988698-0.074162465614-0.0732083400950.110655932927-0.0959572581382-0.055566477590.1289405134570.4536875354720.004842615278540.478004248072-0.0346102531147-0.01933795825370.452498736124-0.02285726295990.42004554987615.50030887770.62600166587942.3705937389
140.760292838718-0.4219372221970.009071697546030.4964632289150.01801606376653.92244078079-0.129810062595-0.2104334014890.1491177298640.1267383517920.0149747164653-0.212638237873-0.3625360560740.3270484529870.1296348160910.556532431117-0.1037065339380.03919438773640.535295323208-0.1052417272960.6344716055882.2405591506618.604745443772.481756081
150.911441849040.5348191162260.5369484476430.751914654820.1752598383621.538160168430.163471199733-0.358923914481-0.2674772111610.206303893012-0.00181084476986-0.2097667631880.373056346311-0.237562786371-0.1353231849420.593979618248-0.110245422153-0.01138407965850.725312761370.01298235580880.575940685677-20.3543381791-7.1180669893466.6967719362
161.858146609330.0968246365896-0.3014673678740.569509410003-0.3449414207831.54109581056-0.02631894700290.0914749953047-0.286974696679-0.1496885714450.1257232538190.1214246994980.500701569144-0.203487324281-0.0939844484760.523761108501-0.152479321062-0.04552005707730.419316698913-0.06340442518740.489059147454-25.6158754036-14.04659729730.511239436
170.869821721741-1.02153708082-0.4204399034252.02610743281-0.8129181288111.850213706070.1866238948790.829367850715-0.868569904176-0.392837744865-0.2130687516690.285433901090.879987632323-1.30174730002-0.1159759245020.813655885796-0.203151424485-0.04139564937881.18976063995-0.2589483634480.76321776776-9.33850996304-15.211651097325.5794487551
183.32376791369-1.32145012158-0.4315005385493.61413815306-0.1610190035130.1538929495660.0229686843639-0.9242878735350.161939388334-0.328511835552-0.0372777169580.1992377049950.112879603492-0.566869555027-0.3184928033490.477571235082-0.01682580650390.05960657868230.688059493027-0.07289433671330.4379040274664.149316078354.3972214411550.1543932782
191.79649588976-0.326777687767-0.9520023561790.932302905968-1.076110695932.288772598720.295799252431-0.698664722275-0.2393056684420.3224740749230.09301738819580.5376380161910.920958390363-0.362638482383-0.4414711726380.707564576774-0.2270138180440.1316548118690.9817260287150.0433685740840.592770126191-10.91570482456.2737123213662.2544335578
200.042317861924-0.0312179930136-0.1396158756870.03450381590030.1433464598780.3611678171610.4156155142680.1583398880280.0925520355794-0.1905465779611.040870845060.0486043581941.15379785468-0.359234372344-1.274512555391.42022613968-0.1484710341430.1691459634371.07803949532-0.07547434367910.873693400182-13.0945117754-0.81398145822978.3515855054
210.160334304960.03173665508870.03427050905520.005840474216370.00229983884110.006992167758070.1807885301950.2162120698350.2762183721371.35013453908E-50.003925316706060.4437772379680.0778486147148-0.702039405608-0.273018956220.649445587511-0.1632571004340.1341709911871.72709592529-0.2110283072380.927202401356-22.466857044910.801548125982.7151012501
223.70965146974-0.849145923496-1.349043293184.633219347950.4010296036863.470361992210.2193728507390.586948818523-1.49411683536-0.469342008228-0.061109437039-0.278008027921.310775126740.22190286566-0.4694798719070.825180329857-0.0822645062519-0.0445735487090.706534280709-0.2113670552350.777168226717-11.7904872144-15.095677601824.1649964485
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 8 )AA-1 - 8
22chain 'A' and (resid 9 through 18 )AA9 - 18
33chain 'A' and (resid 19 through 28 )AA19 - 28
44chain 'A' and (resid 29 through 33 )AA29 - 33
55chain 'A' and (resid 34 through 43 )AA34 - 43
66chain 'A' and (resid 44 through 48 )AA44 - 48
77chain 'A' and (resid 49 through 53 )AA49 - 53
88chain 'A' and (resid 54 through 58 )AA54 - 58
99chain 'A' and (resid 59 through 63 )AA59 - 63
1010chain 'A' and (resid 64 through 68 )AA64 - 68
1111chain 'A' and (resid 69 through 73 )AA69 - 73
1212chain 'A' and (resid 74 through 82 )AA74 - 82
1313chain 'B' and (resid 3 through 445 )BB3 - 4451 - 443
1414chain 'B' and (resid 446 through 653 )BB446 - 653444 - 651
1515chain 'B' and (resid 654 through 1088 )BB654 - 1088652 - 1053
1616chain 'B' and (resid 1089 through 1367 )BB1089 - 13671054 - 1332
1717chain 'C' and (resid -7 through 2 )CC-7 - 2
1818chain 'C' and (resid 3 through 7 )CC3 - 7
1919chain 'C' and (resid 8 through 12 )CC8 - 12
2020chain 'C' and (resid 13 through 17 )CC13 - 17
2121chain 'C' and (resid 18 through 20 )CC18 - 20
2222chain 'D' and (resid -2 through 7 )DD-2 - 7

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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