[English] 日本語
Yorodumi
- PDB-7ox8: Target-bound SpCas9 complex with TRAC full RNA guide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ox8
TitleTarget-bound SpCas9 complex with TRAC full RNA guide
Components
  • CRISPR-associated endonuclease Cas9/Csn1
  • TRAC non-target DNA strand
  • TRAC target DNA strand
  • sgRNASubgenomic mRNA
KeywordsHYDROLASE / Cas9 / CRISPR / sgRNA / TRAC / 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: 2.75 Å
AuthorsDonohoue, P. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.T. / Gibson, J. ...Donohoue, P. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.T. / 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.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)198,77818
Polymers198,2604
Non-polymers51814
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22860 Å2
ΔGint-189 kcal/mol
Surface area76300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.177, 67.549, 187.854
Angle α, β, γ (deg.)90.000, 111.230, 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

-
Components

-
DNA chain , 2 types, 2 molecules CD

#3: DNA chain TRAC target DNA strand


Mass: 8574.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain TRAC non-target DNA strand


Mass: 3677.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
RNA chain / Protein , 2 types, 2 molecules AB

#1: RNA chain sgRNA / Subgenomic mRNA


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: 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

-
Non-polymers , 3 types, 151 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.: 12 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.72 %
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

-
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: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→47.91 Å / Num. obs: 54164 / % possible obs: 98.89 % / Redundancy: 6.8 % / Biso Wilson estimate: 69.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1792 / Net I/σ(I): 8.53
Reflection shellResolution: 2.75→2.848 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.958 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 5394 / CC1/2: 0.6 / % possible all: 99.13

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ5
Resolution: 2.75→47.91 Å / SU ML: 0.4166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 2707 5.01 %
Rwork0.2091 51371 -
obs0.2111 54078 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.25 Å2
Refinement stepCycle: LAST / Resolution: 2.75→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10875 2532 14 137 13558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004213901
X-RAY DIFFRACTIONf_angle_d0.671819268
X-RAY DIFFRACTIONf_chiral_restr0.0432199
X-RAY DIFFRACTIONf_plane_restr0.00362025
X-RAY DIFFRACTIONf_dihedral_angle_d17.43025634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80.47361430.42722725X-RAY DIFFRACTION99.1
2.8-2.850.38711390.37652634X-RAY DIFFRACTION99.14
2.85-2.910.37851500.35342701X-RAY DIFFRACTION99.17
2.91-2.980.36861420.33522703X-RAY DIFFRACTION99.03
2.98-3.040.36561320.32832651X-RAY DIFFRACTION97.99
3.04-3.120.2981420.31412598X-RAY DIFFRACTION96.72
3.12-3.210.33191350.27672726X-RAY DIFFRACTION99.13
3.21-3.30.28561490.2512698X-RAY DIFFRACTION99.3
3.3-3.410.28741420.23232704X-RAY DIFFRACTION99.27
3.41-3.530.27471430.22732691X-RAY DIFFRACTION99.44
3.53-3.670.22991430.21772696X-RAY DIFFRACTION99.2
3.67-3.840.24941430.20822718X-RAY DIFFRACTION99.48
3.84-4.040.23461400.18582687X-RAY DIFFRACTION99.44
4.04-4.290.23811450.1852712X-RAY DIFFRACTION98.93
4.29-4.620.21031400.17612654X-RAY DIFFRACTION96.91
4.62-5.090.20361430.15582750X-RAY DIFFRACTION99.52
5.09-5.820.22711420.16382726X-RAY DIFFRACTION99.27
5.82-7.330.22941490.19182789X-RAY DIFFRACTION99.73
7.33-47.910.19191450.17132808X-RAY DIFFRACTION97.98
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)
10.3300399925910.009986810257150.1459798786040.190001287421-0.0230359823770.585307219277-0.0912511100786-0.1024700452150.0187917047550.117649087980.02343104419480.0262933041008-0.151483668967-0.09796956325177.80538108443E-60.5812110791230.0351747080660.03966161327410.499166655989-0.01429451086240.58176705374-6.324745905519.215772524773.7670397435
20.660991848766-0.5847599985930.09582513732150.367728753786-0.1959778880560.695502014785-0.0397350863168-0.0632160531101-0.119124766630.07189695982290.02014399943950.04637160150040.1309155315860.0421095413155-1.10273980497E-50.607604901113-0.0109132565258-0.02085223083020.572186084251-0.07663517826890.646326299646-11.0439981134-11.920201272866.5411052495
30.5341544310550.06833216482330.04719458336160.2608494079590.02640476965340.400588110071-0.07007668470680.126400722825-0.03927080837260.02237088140450.05802377763470.01456551274040.292114731683-0.2014878315731.54201596235E-60.478993167678-0.1066314363550.03281651759240.405882942209-0.03300437816680.408594610203-29.3028043856-13.763854652640.5248775896
40.0241705303098-0.00607001172118-0.01088550602040.01452635293490.01559355741920.0157627718068-0.06048443331230.151599287869-0.4480544458150.256861087567-0.02904101684880.00521586302013-0.0556250169126-0.3383421564460.0002055530959291.05055490906-0.494320013555-0.02511035574651.81595207332-0.3165970270831.10193650251-15.9935053671-21.4967865719.227642724
50.02354681939080.0132132230576-0.01911888705080.0403153329932-0.04123370690090.04251512367850.198910515449-0.0679742608881-0.2056331433770.167851454863-0.2288128326760.1134343717140.197623955276-0.0297838538853-0.0005437495676250.630475166673-0.0463815093649-0.03887651873290.780605370022-0.1904439991940.692192109051-2.75463188225-9.4011634845531.3053749049
6-0.0492927507-0.0502803021003-0.0414573579997-0.05222671041190.157019622530.0880652942472-0.0244350078674-0.1274330894310.324319137738-0.1268174344430.3798514565510.05543929049580.433105467236-0.03358838239373.52553081223E-50.701866993956-0.05998071167030.04003082102350.7242243827140.04477383467450.619834970671-7.370641327585.281274528765.2717918496
71.02430447216-0.00966607569689-0.6728274560160.003555806835370.01500935889970.4319992551590.4653704235241.04185673704-0.252169735449-0.1752560966420.140234020552-0.113917464190.26044149565-0.1609760281020.09076848785680.666060180743-0.0865417326883-0.03559598286260.765525407333-0.2351654234950.64757277159-11.7293409654-14.315950417923.5671493753
80.102892260143-0.1110620751180.1108475421910.0939904014612-0.09242442256830.101101038978-0.2848164277270.2170236643810.06098942460090.1901087485060.006478431355160.372088325011.03230509244-0.543614995708-0.000289968496740.753718456834-0.09726980695310.04532294652120.755949923753-0.1103326975780.872016579336-15.0114623266.7945641845774.3623593704
9-0.017583778337-0.0225095883759-0.0313298227610.262667794162-0.055926507177-0.02197009848180.0252969114422-0.08147957129760.25671665830.1637859531860.240449636847-0.006954335247540.3039752761470.220017209203-2.16051689536E-50.5804996068620.0106929714919-0.005343439026280.6320378449220.007502062655370.5168166071355.340230321273.8863930977937.1251860876
100.00392107132746-0.0115843590941-0.003644024353860.040469425120.02458167891280.007830313768080.2947397071040.2410637843350.419952176127-0.05461100841280.107907255690.2971670418590.02095131385120.104453321335-0.0008142567548351.147355870850.263489851858-0.09182571974561.30856543354-0.343272758460.84459135926.1889379785-13.02832241213.55851757172
110.01230315398240.01204753497090.01352644401770.0157437899920.01775567135290.02900566514310.09871375738820.05712975725750.176133382584-0.699906431691-0.1016877885160.734174996524-0.197280163527-0.03774238903310.0001554993767351.814169969860.225538983654-0.2438885219511.782709100110.02225570381351.2740573678218.2772462759-18.9008018214-0.442502029479
120.02777303855990.0594816791951-0.05219868998980.0937057798981-0.1310947856110.1802012161970.01469686638970.332690866419-0.0669435639850.06268990254680.06818263767160.2582939812640.253925205-0.1081351360020.0001545273379250.6243102062530.000413988239203-0.05072014235510.594168400939-0.1532954107460.46565283990521.6615970695-5.827555699120.3127734628
130.2120907765050.1815917408990.1334845107270.1590703406590.1396895206850.1528870048940.01006912763390.0482705541806-0.144832108477-0.03748457162410.0146600323940.07771684805880.0413717138017-0.03830156031119.42824920656E-50.5065064838620.0039095571432-0.09725032970830.505302732399-0.0275742117960.512047755813-4.4136255248417.514267859827.8162404011
140.0819010569522-0.13865565837-0.04146266417150.215530037577-0.03975676003230.1597253497820.179844727201-0.2163042687870.3589447511070.251306559141-0.2599138738740.193400886297-0.222601194025-0.2199679210910.0003060382592380.58990576617-0.0485420844744-0.01405211376730.5957217780310.04630123828770.592087623232-14.413152204711.558724618237.2660497827
150.0265125082651-0.02576113067710.01520429383360.02072743410980.004313467878430.01824634111310.318678474530.3821389828330.815858433131-0.2830936668340.02280902896930.34752184811-0.9617312997750.3084274701170.0007528351981471.06416180670.04924398292830.0990879497180.8224628282370.1580900029341.20059746302-40.056224407213.443379167429.6503372525
160.0873319129566-0.09483819392130.05815039128910.0881210528899-0.05837462916730.03212936709460.03130171053220.136157156762-0.228806086345-0.220417270883-0.2744533363520.111676279699-0.5945359349250.1344198170113.7895876001E-51.01420694114-0.1776168312050.0004310862975171.358044388330.0439838038770.987612488908-39.291064312715.730121586936.086044528
170.2186774083090.3058337501850.05467491904350.0781994771565-0.2520278049350.6409348689150.09720100577050.09032539687080.04049973343780.0600405930697-0.0892504705880.0400701818404-0.02011453560530.2248107596541.06542425546E-50.489903432105-0.08125281432710.02284435293490.554357047649-0.05084748972040.5401874107045.781748846166.3529934732937.277558229
180.500265456235-0.4997397597310.7876561042550.271291012995-0.680603104620.899464754216-0.1462245388890.161168835277-0.01440105428020.207714512636-0.0428955528279-0.0639888910602-0.338835309872-0.347719556805-4.56978321688E-50.81400281410.129111566084-0.04136322633050.84542403873-0.1083218818830.76193064665926.1370818467-3.6155441589956.5218694061
190.41311455528-0.215097828248-0.0800023357529-0.028433401768-0.05091586041641.223388367790.04810312650110.009231751558730.06233586338960.0848312366657-0.00836863135685-0.00415378530369-0.1399902472110.144548952801-1.16741117695E-50.350742990356-0.0775879880117-0.01516769255720.439564273460.01378787934260.4268056924369.084878502389.0577454482852.9440972681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 567 through 750 )
2X-RAY DIFFRACTION2chain 'B' and (resid 751 through 953 )
3X-RAY DIFFRACTION3chain 'B' and (resid 954 through 1366 )
4X-RAY DIFFRACTION4chain 'C' and (resid -7 through -3 )
5X-RAY DIFFRACTION5chain 'C' and (resid -2 through 2 )
6X-RAY DIFFRACTION6chain 'C' and (resid 3 through 20 )
7X-RAY DIFFRACTION7chain 'D' and (resid -2 through 7 )
8X-RAY DIFFRACTION8chain 'A' and (resid -1 through 8 )
9X-RAY DIFFRACTION9chain 'A' and (resid 9 through 28 )
10X-RAY DIFFRACTION10chain 'A' and (resid 29 through 33 )
11X-RAY DIFFRACTION11chain 'A' and (resid 34 through 38 )
12X-RAY DIFFRACTION12chain 'A' and (resid 39 through 48 )
13X-RAY DIFFRACTION13chain 'A' and (resid 49 through 58 )
14X-RAY DIFFRACTION14chain 'A' and (resid 59 through 68 )
15X-RAY DIFFRACTION15chain 'A' and (resid 69 through 73 )
16X-RAY DIFFRACTION16chain 'A' and (resid 74 through 82 )
17X-RAY DIFFRACTION17chain 'B' and (resid 3 through 207 )
18X-RAY DIFFRACTION18chain 'B' and (resid 208 through 342 )
19X-RAY DIFFRACTION19chain 'B' and (resid 343 through 566 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more