[English] 日本語
Yorodumi
- PDB-4zt0: Crystal structure of catalytically-active Streptococcus pyogenes ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4zt0
TitleCrystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolution
Components
  • CRISPR-associated endonuclease Cas9
  • single-guide RNA
KeywordsHYDROLASE/RNA / CRISPR-Cas9 / bacteria adaptive immunity / DNA endonuclease / HYDROLASE-RNA complex / genome editing and regulation
Function / homologyCRISPR-associated endonuclease Cas9, PAM-interacting domain / REC lobe of CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain profile. / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / HNH nuclease / CRISPR-associated endonuclease Cas9 / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, bridge helix / CRISPR-associated endonuclease Cas9, REC lobe / Cas9-type HNH domain ...CRISPR-associated endonuclease Cas9, PAM-interacting domain / REC lobe of CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain profile. / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / HNH nuclease / CRISPR-associated endonuclease Cas9 / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, bridge helix / CRISPR-associated endonuclease Cas9, REC lobe / Cas9-type HNH domain / HNH endonuclease / maintenance of CRISPR repeat elements / endodeoxyribonuclease activity / 3'-5' exonuclease activity / defense response to virus / Hydrolases, Acting on ester bonds / RNA binding / DNA binding / metal ion binding / un:a0a0c6fzc2: / CRISPR-associated endonuclease Cas9/Csn1
Function and homology information
Specimen sourceStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.9 Å resolution
AuthorsJiang, F. / Doudna, J.A.
CitationJournal: Science / Year: 2015
Title: A Cas9-guide RNA complex preorganized for target DNA recognition.
Authors: Jiang, F. / Zhou, K. / Ma, L. / Gressel, S. / Doudna, J.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 14, 2015 / Release: Jul 8, 2015

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
B: single-guide RNA
C: CRISPR-associated endonuclease Cas9
D: single-guide RNA


Theoretical massNumber of molelcules
Total (without water)374,6124
Polyers374,6124
Non-polymers00
Water0
1
A: CRISPR-associated endonuclease Cas9
B: single-guide RNA


Theoretical massNumber of molelcules
Total (without water)187,3062
Polyers187,3062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)10840
ΔGint (kcal/M)-103
Surface area (Å2)72470
MethodPISA
2
C: CRISPR-associated endonuclease Cas9
D: single-guide RNA


Theoretical massNumber of molelcules
Total (without water)187,3062
Polyers187,3062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11100
ΔGint (kcal/M)-99
Surface area (Å2)71830
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)103.238, 143.002, 294.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

-
Components

#1: Protein/peptide CRISPR-associated endonuclease Cas9 / Csn1 protein / Cas9 / CRISPR-Cas9


Mass: 159804.594 Da / Num. of mol.: 2 / Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: csn1, cas9, ERS445054_00848, MTB314_0777 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0C6FZC2, UniProt: Q99ZW2*PLUS, Hydrolases, Acting on ester bonds
#2: RNA chain single-guide RNA


Mass: 27501.404 Da / Num. of mol.: 2 / Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.92 / Density percent sol: 57.9 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% w/v PEG8000, 100 mM sodium cacodylate, pH 6.0, 250 mM sodium chloride

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Dec 5, 2014
RadiationMonochromator: double crystal Si(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 75.04 Å2 / D resolution high: 2.9 Å / D resolution low: 102.7 Å / Number all: 97517 / Number obs: 97000 / Rmerge I obs: 0.035 / NetI over sigmaI: 12.9 / Redundancy: 9.8 % / Percent possible obs: 99.4
Reflection shellRmerge I obs: 0.456 / Highest resolution: 2.9 Å / Lowest resolution: 3 Å / MeanI over sigI obs: 1.7 / Redundancy: 6.6 % / Percent possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefineMethod to determine structure: SAD / Overall SU ML: 0.4 / R Free selection details: SAD-MR was used / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 28.81 / Stereochemistry target values: MLHL
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2637 / R factor R work: 0.2382 / R factor obs: 0.2395 / Highest resolution: 2.9 Å / Lowest resolution: 49.153 Å / Number reflection R free: 4800 / Number reflection obs: 96760 / Percent reflection R free: 4.96 / Percent reflection obs: 99.26
Refine hist #LASTHighest resolution: 2.9 Å / Lowest resolution: 49.153 Å
Number of atoms included #LASTProtein: 20700 / Nucleic acid: 3090 / Ligand: 0 / Solvent: 0 / Total: 23790
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224530
X-RAY DIFFRACTIONf_angle_d0.55433892
X-RAY DIFFRACTIONf_dihedral_angle_d12.0699424
X-RAY DIFFRACTIONf_chiral_restr0.0233968
X-RAY DIFFRACTIONf_plane_restr0.0023831
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.90000.37060.35142.9330164282693.00
2.93300.37060.34262.9675136291295.00
2.96750.34750.32553.0037138296597.00
3.00370.38400.31933.0417163301597.00
3.04170.35590.32323.0817150295099.00
3.08170.36560.32233.1239157307699.00
3.12390.35780.31833.1685154299899.00
3.16850.34280.31333.21581773064100.00
3.21580.30470.28793.26601453044100.00
3.26600.28730.27453.31961363098100.00
3.31960.31430.27663.37681683020100.00
3.37680.27310.27643.43821593085100.00
3.43820.32500.25923.50431473043100.00
3.50430.31160.25993.57581653092100.00
3.57580.28450.25073.65351613042100.00
3.65350.27500.25143.73851623071100.00
3.73850.26990.23833.83201663089100.00
3.83200.24290.22663.93551723028100.00
3.93550.23040.22424.05131853071100.00
4.05130.24730.21824.18201633064100.00
4.18200.24690.21164.33141523115100.00
4.33140.20350.20674.50471533099100.00
4.50470.19370.19454.70951503082100.00
4.70950.22120.20274.95761463130100.00
4.95760.25090.20205.26791663088100.00
5.26790.27780.22475.67411873115100.00
5.67410.27110.23306.24411643128100.00
6.24410.25590.23917.14521583166100.00
7.14520.21730.21218.99321673192100.00
8.99320.25110.226849.1599189329299.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.42680.31200.12921.4205-0.42960.5619-0.2213-0.0072-0.1818-0.1668-0.3849-0.71330.39910.3369-0.41150.49180.28730.15660.62430.65960.851241.7600-4.2478-40.5455
21.3225-0.40300.63301.7162-0.35941.7197-0.20590.33070.3377-0.7795-0.3913-0.58810.34120.02280.08150.68190.12150.17020.61710.18100.676435.4728-0.1983-57.1491
30.2159-0.6645-0.15154.7488-1.51791.84540.11460.1786-0.0468-0.7139-0.05960.2055-0.01290.0901-0.04020.5629-0.0804-0.09090.63800.13010.55870.058715.5370-46.1095
41.7630-0.48060.15122.3799-0.51361.5282-0.2033-0.17940.16550.45900.10370.1419-0.16600.24250.12060.4820-0.05420.03360.43540.05120.37048.29186.5164-18.8585
56.97160.82040.47811.66711.15692.1217-0.4529-0.39550.4024-0.3363-0.1770-0.9981-0.31480.40820.19220.7046-0.03570.03840.85320.48201.011747.1143-6.3807-33.7753
63.1247-0.02670.59891.31170.51550.32010.3936-1.7935-0.56690.1653-0.42440.47400.3735-0.3881-0.27101.7825-0.7274-1.15073.22980.66792.953474.03235.0047-4.0826
70.8173-0.2589-1.90135.25544.46137.28200.2725-0.0416-0.27360.85001.1362-1.06800.32491.4519-1.11080.9822-0.0764-0.58921.36880.48792.136469.19774.4133-24.3621
80.3909-0.54310.25221.19550.07840.7916-0.2543-0.3353-0.52460.0314-0.2736-0.42390.36980.2130-0.02250.68520.09900.22350.64430.39050.776534.2704-17.5727-30.7422
98.6079-1.67131.16498.41410.84108.41250.37050.7050-0.4279-0.0463-0.25570.08360.59270.1844-0.12290.74300.07080.16370.40990.08100.62853.5676-23.1544-22.1680
105.3712-0.65571.81410.8331-0.26831.5836-0.04260.26300.02540.2044-0.07270.0814-0.1391-0.08430.11930.7766-0.0052-0.03650.4466-0.05630.327415.3563-53.9147-29.0622
110.9806-1.3957-0.65345.46791.43781.6471-0.04150.0946-0.2086-0.5407-0.0402-0.1381-0.0333-0.13980.06810.5172-0.10320.03050.3849-0.13970.40146.1833-75.0843-52.8551
123.60600.8299-3.30102.7834-1.25825.2039-0.56400.3081-1.13420.2474-0.07150.59380.0682-0.43620.54630.6523-0.05340.13880.5993-0.06250.8421-7.1071-74.4509-37.2102
132.2076-0.1692-0.22571.7521-0.53361.6120-0.24760.6654-0.1459-0.15080.09620.37620.1476-0.29310.06550.5606-0.02930.02020.5302-0.16610.4392-5.5213-59.6677-44.5666
144.0780-2.1691-3.02204.94934.08835.8544-0.32480.7494-0.4718-0.4126-0.05010.08410.0263-0.08680.21920.6930-0.21770.14930.9126-0.06170.552226.4197-62.8746-66.4253
151.47621.03961.94791.02410.39374.9320-0.18380.6554-0.4040-0.23130.2427-0.3926-0.55290.7088-0.07220.65070.06110.00981.1530-0.09610.705244.5602-61.2544-53.4886
161.2719-1.51490.11522.5628-0.17172.63870.34070.9671-1.2276-0.5664-0.27100.19940.97570.2142-0.06141.25570.1827-0.17321.7707-0.52111.455849.8154-88.6219-43.7345
172.6052-0.11001.11380.6845-0.85001.2247-0.18890.1876-0.47830.16180.0359-0.20780.00020.1086-0.08500.78190.0980-0.16000.6456-0.17990.584544.2556-68.8268-19.5998
184.2788-1.49070.46662.06241.98964.1910-0.1709-0.5358-0.58950.7281-0.04690.82300.3198-0.85360.23420.6113-0.0887-0.11020.63450.04090.476941.0367-76.4040-8.8482
195.0919-0.0352-3.13421.68740.31215.6360-0.6167-0.3738-0.40940.24520.22820.19230.6197-0.10070.40170.79840.05490.01790.5769-0.00000.43373.4951-60.1331-31.4762
203.4455-2.6756-4.40274.93472.64355.9504-0.1137-1.6802-0.13352.69900.91950.6218-0.4271-0.4146-0.74541.93450.06190.40001.51970.16231.1709-19.6483-70.6472-0.6081
214.4507-0.0414-2.28951.93893.60717.8028-0.1749-0.7456-1.10420.97610.16980.64171.2527-0.29360.12131.20630.12560.57391.11380.22681.0561-17.9946-72.5378-19.2566
222.3848-0.21201.00400.8343-0.30290.4928-0.2646-0.24880.33590.33490.0896-0.0984-0.07100.05500.15860.78920.0943-0.11210.6282-0.12700.420016.6467-48.8408-29.6761
237.39402.19131.62111.3618-1.53025.98760.09351.27060.70810.4251-0.60920.0349-1.07590.41100.42681.48820.1054-0.41870.75510.13571.132248.4636-42.2518-22.2984
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 255 )
2X-RAY DIFFRACTION2chain 'A' and (resid 256 through 712 )
3X-RAY DIFFRACTION3chain 'A' and (resid 713 through 1018 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1019 through 1366 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 38 )
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 45 )
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 68 )
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 82 )
10X-RAY DIFFRACTION10chain 'C' and (resid 4 through 150 )
11X-RAY DIFFRACTION11chain 'C' and (resid 151 through 283 )
12X-RAY DIFFRACTION12chain 'C' and (resid 284 through 376 )
13X-RAY DIFFRACTION13chain 'C' and (resid 377 through 455 )
14X-RAY DIFFRACTION14chain 'C' and (resid 456 through 653 )
15X-RAY DIFFRACTION15chain 'C' and (resid 654 through 750 )
16X-RAY DIFFRACTION16chain 'C' and (resid 751 through 980 )
17X-RAY DIFFRACTION17chain 'C' and (resid 981 through 1280 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1281 through 1366 )
19X-RAY DIFFRACTION19chain 'D' and (resid 11 through 31 )
20X-RAY DIFFRACTION20chain 'D' and (resid 32 through 37 )
21X-RAY DIFFRACTION21chain 'D' and (resid 38 through 44 )
22X-RAY DIFFRACTION22chain 'D' and (resid 45 through 68 )
23X-RAY DIFFRACTION23chain 'D' and (resid 69 through 82 )

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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