[English] 日本語
Yorodumi
- EMDB-76400: Cryo-EM structure of dCas9 bound to DNA duplex with 9 bp extension -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76400
TitleCryo-EM structure of dCas9 bound to DNA duplex with 9 bp extension
Map data
Sample
  • Complex: Catalytically inactive Cas9 complexed with guide RNA and target DNA duplex
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • RNA: Guide RNA
    • DNA: Target DNA, strand 1
    • DNA: Target DNA, strand 2
KeywordsCas9 / DNA BINDING PROTEIN
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, bridge helix / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 ...CRISPR-associated endonuclease Cas9, bridge helix / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas9/Csn1
Similarity search - Component
Biological speciesStreptococcus pyogenes M1 GAS (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGrassetti AV / Kinman LF / Davis JH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144542 United States
National Science Foundation (NSF, United States)2046778 United States
CitationJournal: To Be Published
Title: Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryo-EM reconstruction methods
Authors: Grassetti AV / Kinman LF / Davis JH
History
DepositionApr 2, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76400.png

Downloads & links

-
Map

FileDownload / File: emd_76400.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 256 pix.
= 287.168 Å		1.12 Å/pix.
x 256 pix.
= 287.168 Å		1.12 Å/pix.
x 256 pix.
= 287.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12175 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.5433852 - 1.815496
Average (Standard dev.)-0.0011658658 (±0.034016207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 287.168 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_76400_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_76400_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Catalytically inactive Cas9 complexed with guide RNA and target D...

EntireName: Catalytically inactive Cas9 complexed with guide RNA and target DNA duplex
Components
  • Complex: Catalytically inactive Cas9 complexed with guide RNA and target DNA duplex
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • RNA: Guide RNA
    • DNA: Target DNA, strand 1
    • DNA: Target DNA, strand 2

-
Supramolecule #1: Catalytically inactive Cas9 complexed with guide RNA and target D...

SupramoleculeName: Catalytically inactive Cas9 complexed with guide RNA and target DNA duplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Macromolecule #1: CRISPR-associated endonuclease Cas9

MacromoleculeName: CRISPR-associated endonuclease Cas9 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes M1 GAS (bacteria)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: SNACDKKYSI GLAIGTNSVG WAVITDEYKV PSKKFKVLGN TDRHSIKKNL IGALLFDSGE TAEATRLKRT ARRRYTRRKN RISYLQEIFS NEMAKVDDSF FHRLEESFLV EEDKKHERHP IFGNIVDEVA YHEKYPTIYH LRKKLVDSTD KADLRLIYLA LAHMIKFRGH ...String:
SNACDKKYSI GLAIGTNSVG WAVITDEYKV PSKKFKVLGN TDRHSIKKNL IGALLFDSGE TAEATRLKRT ARRRYTRRKN RISYLQEIFS NEMAKVDDSF FHRLEESFLV EEDKKHERHP IFGNIVDEVA YHEKYPTIYH LRKKLVDSTD KADLRLIYLA LAHMIKFRGH FLIEGDLNPD NSDVDKLFIQ LVQTYNQLFE ENPINASGVD AKAILSARLS KSRRLENLIA QLPGEKKNGL FGNLIALSLG LTPNFKSNFD LAEDAKLQLS KDTYDDDLDN LLAQIGDQYA DLFLAAKNLS DAILLSDILR VNTEITKAPL SASMIKRYDE HHQDLTLLKA LVRQQLPEKY KEIFFDQSKN GYAGYIDGGA SQEEFYKFIK PILEKMDGTE ELLVKLNRED LLRKQRTFDN GSIPHQIHLG ELHAILRRQE DFYPFLKDNR EKIEKILTFR IPYYVGPLAR GNSRFAWMTR KSEETITPWN FEEVVDKGAS AQSFIERMTN FDKNLPNEKV LPKHSLLYEY FTVYNELTKV KYVTEGMRKP AFLSGEQKKA IVDLLFKTNR KVTVKQLKED YFKKIESFDS VEISGVEDRF NASLGTYHDL LKIIKDKDFL DNEENEDILE DIVLTLTLFE DREMIEERLK TYAHLFDDKV MKQLKRRRYT GWGRLSRKLI NGIRDKQSGK TILDFLKSDG FANRNFMQLI HDDSLTFKED IQKAQVSGQG DSLHEHIANL AGSPAIKKGI LQTVKVVDEL VKVMGRHKPE NIVIEMAREN QTTQKGQKNS RERMKRIEEG IKELGSQILK EHPVENTQLQ NEKLYLYYLQ NGRDMYVDQE LDINRLSDYD VDAIVPQSFL KDDSIDNKVL TRSDKNRGKS DNVPSEEVVK KMKNYWRQLL NAKLITQRKF DNLTKAERGG LSELDKAGFI KRQLVETRQI TKHVAQILDS RMNTKYDEND KLIREVKVIT LKSKLVSDFR KDFQFYKVRE INNYHHAHDA YLNAVVGTAL IKKYPKLESE FVYGDYKVYD VRKMIAKSEQ EIGKATAKYF FYSNIMNFFK TEITLANGEI RKRPLIETNG ETGEIVWDKG RDFATVRKVL SMPQVNIVKK TEVQTGGFSK ESILPKRNSD KLIARKKDWD PKKYGGFDSP TVAYSVLVVA KVEKGKSKKL KSVKELLGIT IMERSSFEKN PIDFLEAKGY KEVKKDLIIK LPKYSLFELE NGRKRMLASA GELQKGNELA LPSKYVNFLY LASHYEKLKG SPEDNEQKQL FVEQHKHYLD EIIEQISEFS KRVILADANL DKVLSAYNKH RDKPIREQAE NIIHLFTLTN LGAPAAFKYF DTTIDRKRYT STKEVLDATL IHQSITGLYE TRIDLSQLGG D

UniProtKB: CRISPR-associated endonuclease Cas9/Csn1

-
Macromolecule #2: Guide RNA

MacromoleculeName: Guide RNA / type: rna / ID: 2
SequenceString:
GACGCAUAAA GAUGAGACGC GUUUUAGAGC UAGAAAUAGC AAGUUAAAAU AAGGCUAGUC CGUUAUCAAC UUGAAAAAGU GGCACCGAGU CGGUGCUU

-
Macromolecule #3: Target DNA, strand 1

MacromoleculeName: Target DNA, strand 1 / type: dna / ID: 3 / Classification: DNA
SequenceString:
TGCTGACGCA TAAAGATGAG ACGCTGGTAA AAAAAA

-
Macromolecule #4: Target DNA, strand 2

MacromoleculeName: Target DNA, strand 2 / type: dna / ID: 4 / Classification: DNA
SequenceString:
TTTTTTTTAC CAGCGTCTCA TCTTTATGCG TCAGCA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHEPES
100.0 mMPotassium chloride
5.0 mMMagnesium chloride
1.0 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 4.45 sec. / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 120000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 261551
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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