[English] 日本語
Yorodumi
- EMDB-17702: Cas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17702
TitleCas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system
Map dataMap sharpened using phenix.auto_sharpen_1.21rc1-4903 using _iso_to_d_cut procedure and 3.24A cutoff.
Sample
  • Complex: Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex
    • Complex: CRISPR-associated endonuclease Cas9
      • Protein or peptide: CRISPR-associated endonuclease Cas9
    • Complex: crRNA, chain B and tracrRNA, chain C
      • RNA: crRNA, chain B
      • RNA: tracrRNA, chain C
    • Complex: DNA oligoduplex, target strand, chains D,E and DNA oligoduplex, non-target strand, chain F
      • DNA: DNA oligoduplex, target strand, chains D,E
      • DNA: DNA oligoduplex, non-target strand, chain F
  • Ligand: MAGNESIUM ION
KeywordsCas9 / CRISPR-Cas / PAM / spacer acquisition / RNA BINDING PROTEIN
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / 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
CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesStreptococcus thermophilus DGCC 7710 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsSasnauskas G / Gaizauskaite U / Tamulaitiene G
Funding supportLithuania, 1 items
OrganizationGrant numberCountry
Research Council of LithuaniaS-MIP-19-32Lithuania
CitationJournal: To Be Published
Title: Structural basis for spacer acquisition in a type II-A CRISPR-Cas system
Authors: Sasnauskas G / Gaizauskaite U / Tamulaitiene G
History
DepositionJun 23, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17702.png

Downloads & links

-
Map

FileDownload / File: emd_17702.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpened using phenix.auto_sharpen_1.21rc1-4903 using _iso_to_d_cut procedure and 3.24A cutoff.
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-22.785442 - 35.520446999999997
Average (Standard dev.)0.00000000000844 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_17702_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex

EntireName: Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex
Components
  • Complex: Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex
    • Complex: CRISPR-associated endonuclease Cas9
      • Protein or peptide: CRISPR-associated endonuclease Cas9
    • Complex: crRNA, chain B and tracrRNA, chain C
      • RNA: crRNA, chain B
      • RNA: tracrRNA, chain C
    • Complex: DNA oligoduplex, target strand, chains D,E and DNA oligoduplex, non-target strand, chain F
      • DNA: DNA oligoduplex, target strand, chains D,E
      • DNA: DNA oligoduplex, non-target strand, chain F
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex

SupramoleculeName: Complex of Cas9 bound to crRNA:tracrRNA and to a cognate DNA duplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

+
Supramolecule #2: CRISPR-associated endonuclease Cas9

SupramoleculeName: CRISPR-associated endonuclease Cas9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Streptococcus thermophilus DGCC 7710 (bacteria)

+
Supramolecule #3: crRNA, chain B and tracrRNA, chain C

SupramoleculeName: crRNA, chain B and tracrRNA, chain C / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Streptococcus thermophilus DGCC 7710 (bacteria)

+
Supramolecule #4: DNA oligoduplex, target strand, chains D,E and DNA oligoduplex, n...

SupramoleculeName: DNA oligoduplex, target strand, chains D,E and DNA oligoduplex, non-target strand, chain F
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: synthetic construct (others)

+
Macromolecule #1: CRISPR-associated endonuclease Cas9

MacromoleculeName: CRISPR-associated endonuclease Cas9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Streptococcus thermophilus DGCC 7710 (bacteria)
Molecular weightTheoretical: 162.498531 KDa
Recombinant expressionOrganism: Escherichia coli str. K-12 substr. DH10B (bacteria)
SequenceString: MTKPYSIGLD IGTNSVGWAV ITDNYKVPSK KMKVLGNTSK KYIKKNLLGV LLFDSGITAE GRRLKRTARR RYTRRRNRIL YLQEIFSTE MATLDDAFFQ RLDDSFLVPD DKRDSKYPIF GNLVEEKVYH DEFPTIYHLR KYLADSTKKA DLRLVYLALA H MIKYRGHF ...String:
MTKPYSIGLD IGTNSVGWAV ITDNYKVPSK KMKVLGNTSK KYIKKNLLGV LLFDSGITAE GRRLKRTARR RYTRRRNRIL YLQEIFSTE MATLDDAFFQ RLDDSFLVPD DKRDSKYPIF GNLVEEKVYH DEFPTIYHLR KYLADSTKKA DLRLVYLALA H MIKYRGHF LIEGEFNSKN NDIQKNFQDF LDTYNAIFES DLSLENSKQL EEIVKDKISK LEKKDRILKL FPGEKNSGIF SE FLKLIVG NQADFRKCFN LDEKASLHFS KESYDEDLET LLGYIGDDYS DVFLKAKKLY DAILLSGFLT VTDNETEAPL SSA MIKRYN EHKEDLALLK EYIRNISLKT YNEVFKDDTK NGYAGYIDGK TNQEDFYVYL KNLLAEFEGA DYFLEKIDRE DFLR KQRTF DNGSIPYQIH LQEMRAILDK QAKFYPFLAK NKERIEKILT FRIPYYVGPL ARGNSDFAWS IRKRNEKITP WNFED VIDK ESSAEAFINR MTSFDLYLPE EKVLPKHSLL YETFNVYNEL TKVRFIAESM RDYQFLDSKQ KKDIVRLYFK DKRKVT DKD IIEYLHAIYG YDGIELKGIE KQFNSSLSTY HDLLNIINDK EFLDDSSNEA IIEEIIHTLT IFEDREMIKQ RLSKFEN IF DKSVLKKLSR RHYTGWGKLS AKLINGIRDE KSGNTILDYL IDDGISNRNF MQLIHDDALS FKKKIQKAQI IGDEDKGN I KEVVKSLPGS PAIKKGILQS IKIVDELVKV MGGRKPESIV VEMARENQYT NQGKSNSQQR LKRLEKSLKE LGSKILKEN IPAKLSKIDN NALQNDRLYL YYLQNGKDMY TGDDLDIDRL SNYDIDHIIP QAFLKDNSID NKVLVSSASN RGKSDDFPSL EVVKKRKTF WYQLLKSKLI SQRKFDNLTK AERGGLLPED KAGFIQRQLV ETRQITKHVA RLLDEKFNNK KDENNRAVRT V KIITLKST LVSQFRKDFE LYKVREINDF HHAHDAYLNA VIASALLKKY PKLEPEFVYG DYPKYNSFRE RKSATEKVYF YS NIMNIFK KSISLADGRV IERPLIEVNE ETGESVWNKE SDLATVRRVL SYPQVNVVKK VEEQNHGLDR GKPKGLFNAN LSS KPKPNS NENLVGAKEY LDPKKYGGYA GISNSFAVLV KGTIEKGAKK KITNVLEFQG ISILDRINYR KDKLNFLLEK GYKD IELII ELPKYSLFEL SDGSRRMLAS ILSTNNKRGE IHKGNQIFLS QKFVKLLYHA KRISNTINEN HRKYVENHKK EFEEL FYYI LEFNENYVGA KKNGKLLNSA FQSWQNHSID ELCSSFIGPT GSERKGLFEL TSRGSAADFE FLGVKIPRYR DYTPSS LLK DATLIHQSVT GLYETRIDLA KLGEGLEGHH HHHH

UniProtKB: CRISPR-associated endonuclease Cas9

+
Macromolecule #2: crRNA, chain B

MacromoleculeName: crRNA, chain B / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Streptococcus thermophilus DGCC 7710 (bacteria)
Molecular weightTheoretical: 13.609083 KDa
SequenceString:
CGCUAAAGAG GAAGAGGACA GUUUUAGAGC UGUGUUGUUU CG

+
Macromolecule #3: tracrRNA, chain C

MacromoleculeName: tracrRNA, chain C / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Streptococcus thermophilus DGCC 7710 (bacteria)
Molecular weightTheoretical: 24.119357 KDa
SequenceString:
CGAAACAACA CAGCGAGUUA AAAUAAGGCU UAGUCCGUAC UCAACUUGAA AAGGUGGCAC CGAUUCGGUG UUUUU

GENBANK: GENBANK: HQ712120.1

+
Macromolecule #4: DNA oligoduplex, target strand, chains D,E

MacromoleculeName: DNA oligoduplex, target strand, chains D,E / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.670199 KDa
SequenceString:
(DG)(DC)(DT)(DG)(DA)(DC)(DT)(DC)(DA)(DC) (DC)(DA)(DT)(DG)(DT)(DC)(DC)(DT)(DC)(DT) (DT)(DC)(DC)(DT)(DC)(DT)(DT)(DT)(DA) (DG)(DC)(DG)

+
Macromolecule #5: DNA oligoduplex, non-target strand, chain F

MacromoleculeName: DNA oligoduplex, non-target strand, chain F / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.718427 KDa
SequenceString:
(DT)(DG)(DG)(DT)(DG)(DA)(DG)(DT)(DC)(DA) (DG)(DC)

+
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1744 / Average exposure time: 46.33 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 894269 / Details: Blob picking in cryoSPARC live session
Startup modelType of model: INSILICO MODEL / In silico model: ab-initio cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 119790
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8pj9:
Cas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system

+
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://pdbjlvh1.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