[English] 日本語
Yorodumi
- PDB-7qqx: SpCas9 bound to FANCF off-target5 DNA substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qqx
TitleSpCas9 bound to FANCF off-target5 DNA substrate
Components
  • (FANCF off-target5 ...) 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 / 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: 2.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FANCF sgRNA
B: CRISPR-associated endonuclease Cas9/Csn1
C: FANCF off-target5 target strand
D: FANCF off-target5 non-target strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,40515
Polymers198,0054
Non-polymers40011
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21710 Å2
ΔGint-173 kcal/mol
Surface area76970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.534, 67.378, 188.387
Angle α, β, γ (deg.)90.000, 110.903, 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

-
FANCF off-target5 ... , 2 types, 2 molecules CD

#3: DNA chain FANCF off-target5 target strand


Mass: 8685.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain FANCF off-target5 non-target strand


Mass: 3662.404 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 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

-
Non-polymers , 3 types, 535 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.: 9 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.64 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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.94 Å / Num. obs: 81607 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 53.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 1 / Num. unique obs: 8058 / CC1/2: 0.438 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ5
Resolution: 2.4→48 Å / SU ML: 0.3483 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 4091 5.02 %
Rwork0.1822 77473 -
obs0.1839 81564 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10919 2547 11 524 14001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003513963
X-RAY DIFFRACTIONf_angle_d0.623919357
X-RAY DIFFRACTIONf_chiral_restr0.03952209
X-RAY DIFFRACTIONf_plane_restr0.00312034
X-RAY DIFFRACTIONf_dihedral_angle_d18.44965666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.35811470.32482604X-RAY DIFFRACTION98.78
2.43-2.460.32881430.32032659X-RAY DIFFRACTION98.94
2.46-2.490.34421360.30962661X-RAY DIFFRACTION98.73
2.49-2.520.33181390.30182602X-RAY DIFFRACTION98.31
2.52-2.560.32411310.28632598X-RAY DIFFRACTION97.81
2.56-2.590.31091560.27782671X-RAY DIFFRACTION98.13
2.59-2.630.34511370.27362644X-RAY DIFFRACTION99.39
2.63-2.670.33781380.2722646X-RAY DIFFRACTION99.25
2.67-2.720.30931340.26352681X-RAY DIFFRACTION99.29
2.72-2.760.3631450.26052630X-RAY DIFFRACTION99.36
2.76-2.810.28661390.25862721X-RAY DIFFRACTION99.41
2.81-2.870.31361440.24192612X-RAY DIFFRACTION99.1
2.87-2.930.29241460.24522695X-RAY DIFFRACTION99.65
2.93-2.990.28531350.24622668X-RAY DIFFRACTION99.57
2.99-3.060.28391460.2332684X-RAY DIFFRACTION99.79
3.06-3.140.26811350.22392664X-RAY DIFFRACTION99.61
3.14-3.220.27121400.20662696X-RAY DIFFRACTION99.58
3.22-3.320.21911440.19532634X-RAY DIFFRACTION99.61
3.32-3.420.23121400.18652692X-RAY DIFFRACTION99.33
3.42-3.540.22311460.19092709X-RAY DIFFRACTION98.96
3.54-3.690.20181330.17472612X-RAY DIFFRACTION97.97
3.69-3.850.18451340.16012668X-RAY DIFFRACTION98.38
3.85-4.060.16871500.14372681X-RAY DIFFRACTION99.89
4.06-4.310.15931340.13562710X-RAY DIFFRACTION99.75
4.31-4.640.15581440.13162693X-RAY DIFFRACTION99.58
4.64-5.110.15751440.1262707X-RAY DIFFRACTION99.34
5.11-5.850.19371430.14612712X-RAY DIFFRACTION99.24
5.85-7.360.18921420.16392698X-RAY DIFFRACTION97.59
7.37-480.16921460.14972821X-RAY DIFFRACTION99.46
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)
10.204040107141-0.228414249717-0.3178337655170.4462077343860.7702215548153.23961321860.0116888980625-0.012759207090.06456961793170.186889375927-0.008556144628340.01068533227560.355716149431-0.223569499720.00576628289630.44580975659-0.07846532678210.02045025145280.430235541275-0.01260666960380.428804553429-1.090948364264.8880958210649.8004590118
21.827927869580.07389536400770.3327243214370.607016407544-0.2716470617761.161726615780.2020546058270.347733677262-0.21853876271-0.217180878875-0.1026032369170.01193955732740.1038279497750.202131343422-0.09726511254360.376590237023-0.00692741869494-0.07379136097810.386614838315-0.03267546545410.3195288287516.722051358571.6981775160121.7689070059
31.30194451101-1.638794666440.3023028581382.289588459570.5299771261313.430307099581.03200095973-1.010468153961.683402865850.590245985371-0.6515317152660.0902138867208-2.620008124840.863190908204-0.08060020381631.40748597169-0.3437823439080.2708237732611.017517597220.02060455457481.29694688872-39.194201799814.740064521534.2058004294
40.7371002060990.244121162198-0.1159208743070.330133356426-0.1757010701160.7803110611130.07002040898750.1068363142650.01969644688710.0768089229259-0.06772492319-0.0502323932539-0.02539002338240.211567475412-0.001196114541150.347116206936-0.0598577696422-0.01438332927020.329292708349-0.0159099298060.3300176339076.117085595576.354698150837.6213691562
53.58978984748-0.7288378201-0.4760387040132.99060151336-0.2015702932644.43798215996-0.02838530536580.261893243475-0.02966510933550.109800307291-0.06411136535750.487972275481-0.44911528577-0.8106173280960.08200554962480.7044897620450.0796826703381-0.03015079347250.622462032503-0.03378477604580.6215509029524.0253412132-3.6519379736767.3946664752
61.28731307544-0.0565056140276-0.307030993231.171199610340.4963828769391.501722632540.0478673618199-0.151720992325-0.198837870540.254004490322-0.0273781654807-0.1594160825790.163089003910.447791430286-0.03678296416030.395405126765-0.0326703472189-0.07235760829310.4978784727110.06704745319170.37473094586619.91427743493.3461754291538.837635075
71.665955491810.223481477049-0.6831273759841.23149231389-0.9634422314092.87229266951-0.0790561873637-0.04724964802180.03190166784120.1400272945590.0154138433326-0.171587302513-0.191058042170.1194855714240.05607794999480.4096428937110.00343514861684-0.05741952809040.287355875109-0.04016942509660.3615762362840.74259369124819.10876859980.8690606501
80.5306549748860.1554487427590.7288508223780.448779222941-0.239276663511.17682314214-0.02179110000720.011436624591-0.02058958361020.00446836411314-0.04741923398210.004771378570210.04883396955130.01418192214450.07788236654810.401189361624-0.02869854513820.06651687320610.4192797471730.0206965355240.421008456094-16.59642551214.768533410762.8346223881
91.40745340215-0.649218432053-0.2665288466481.917831166370.09347893571311.76188988427-0.0328654041835-0.143511968851-0.1334106469970.0477564601163-0.0009386250325110.0745304214959-0.03666448957860.01695879066370.008414325864320.611861137330.0147341614199-0.07290065980720.565377400553-0.03448281159810.643729954817-2.828548411-19.098033815271.7429834921
101.116746110460.237398127452-0.5468575956880.400273375485-0.004973397673951.91517666219-0.1315841998220.0452456427934-0.2183063963950.03170122817310.0433747821358-0.003288284781030.594126567776-0.2301280341430.07855512075250.440731704353-0.0857520551633-0.01132252287260.290612824794-0.01275220588860.406246413481-29.2431609056-12.127984697443.8091513442
114.735308310261.197271982361.471546767541.7436072579-1.408692158832.65728561260.1216834296210.945709628703-0.376498228131-0.1877855975930.2829013226040.919967122960.400766819803-1.449480310960.09472093243621.44435375536-0.7250342905790.1323046468762.17257563139-0.5391634655411.06807824279-16.1180212383-20.103141259318.7101571037
120.9583689960730.23485384610.2941954644570.711705142640.7802803031091.047717398580.289509809924-0.343499609975-0.1731928462760.39799409752-0.297878438470.1148005503550.646234964073-0.1963297731480.04095188784650.554239841404-0.0801600976443-0.05123288143140.5676735331550.02325934656820.4410644442232.08918805589-2.8116115973840.3829209037
130.6181084286260.2442639173830.1766365246920.0631122297762-0.08634665990741.805379540970.0713882628021-0.06706854656230.235520002078-0.01844558111040.2207520545870.1523775879770.075161020364-0.0624213039183-0.3650390230640.567851178631-0.09818286453830.04992783278770.5680663990220.03749790287610.505994348608-11.97224719225.8568661889871.8499285419
144.18974733895-0.260276617411-1.671376996894.734062889130.8748701686955.07343307729-0.108709836180.661177475674-1.11143934486-0.09519107526350.31492967579-0.1585067092651.31279207590.241012935643-0.3960989062940.663865061524-0.0698995408133-0.004768977122730.645270269705-0.211511582490.727221002742-11.4292736531-14.433077446623.9093068619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 82 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 207 )
5X-RAY DIFFRACTION5chain 'B' and (resid 208 through 286 )
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 493 )
7X-RAY DIFFRACTION7chain 'B' and (resid 494 through 678 )
8X-RAY DIFFRACTION8chain 'B' and (resid 679 through 808 )
9X-RAY DIFFRACTION9chain 'B' and (resid 809 through 909 )
10X-RAY DIFFRACTION10chain 'B' and (resid 910 through 1366 )
11X-RAY DIFFRACTION11chain 'C' and (resid -7 through -3 )
12X-RAY DIFFRACTION12chain 'C' and (resid -2 through 7 )
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 20 )
14X-RAY DIFFRACTION14chain 'D' and (resid -2 through 7 )

+
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