[English] 日本語
Yorodumi
- EMDB-43771: CryoEM structure of ThermoCas9 in pre-cleavage state bound with t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43771
TitleCryoEM structure of ThermoCas9 in pre-cleavage state bound with the DNA containing NNNNCCA PAM
Map data
Sample
  • Complex: Ternary complex of ThermoCas9 with single guide RNA and target DNA
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • DNA: non-target DNA
    • DNA: target-strand DNA
    • RNA: single guide RNA
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsCRISPR-Cas9 / Cas9 / Epigenetics / endonuclease / HNH / RuvC / metal binding / RNA / DNA BINDING PROTEIN-DNA-RNA complex
Function / homology:
Function and homology information
Biological speciesGeobacillus thermodenitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsZhao Y / Shu Y / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099604 United States
CitationJournal: To be Published
Title: Molecular Basis for Epigenetic-sensitive Editing by Cas9
Authors: Roth M / Shu Y / Trasanidou D / Zhao Y / van der Oost J / Li H
History
DepositionFeb 22, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43771.png

Downloads & links

-
Map

FileDownload / File: emd_43771.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-2.3737116 - 4.3119698
Average (Standard dev.)0.0015839192 (±0.08817417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_43771_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43771_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of ThermoCas9 with single guide RNA and target DNA

EntireName: Ternary complex of ThermoCas9 with single guide RNA and target DNA
Components
  • Complex: Ternary complex of ThermoCas9 with single guide RNA and target DNA
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • DNA: non-target DNA
    • DNA: target-strand DNA
    • RNA: single guide RNA
  • Ligand: SODIUM ION
  • Ligand: water

-
Supramolecule #1: Ternary complex of ThermoCas9 with single guide RNA and target DNA

SupramoleculeName: Ternary complex of ThermoCas9 with single guide RNA and target DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Geobacillus thermodenitrificans (bacteria)

-
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: Geobacillus thermodenitrificans (bacteria)
Molecular weightTheoretical: 126.563461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKYKIGLDIG ITSIGWAVIN LDIPRIEDLG VRIFDRAENP KTGESLALPR RLARSARRRL RRRKHRLERI RRLFVREGIL TKEELNKLF EKKHEIDVWQ LRVEALDRKL NNDELARILL HLAKRRGFRS NRKSERTNKE NSTMLKHIEE NQSILSSYRT V AEMVVKDP ...String:
MKYKIGLDIG ITSIGWAVIN LDIPRIEDLG VRIFDRAENP KTGESLALPR RLARSARRRL RRRKHRLERI RRLFVREGIL TKEELNKLF EKKHEIDVWQ LRVEALDRKL NNDELARILL HLAKRRGFRS NRKSERTNKE NSTMLKHIEE NQSILSSYRT V AEMVVKDP KFSLHKRNKE DNYTNTVARD DLEREIKLIF AKQREYGNIV CTEAFEHEYI SIWASQRPFA SKDDIEKKVG FC TFEPKEK RAPKATYTFQ SFTVWEHINK LRLVSPGGIR ALTDDERRLI YKQAFHKNKI TFHDVRTLLN LPDDTRFKGL LYD RNTTLK ENEKVRFLEL GAYHKIRKAI DSVYGKGAAK SFRPIDFDTF GYALTMFKDD TDIRSYLRNE YEQNGKRMEN LADK VYDEE LIEELLNLSF SKFGHLSLKA LRNILPYMEQ GEVYSTACER AGYTFTGPKK KQKTVLLPNI PPIANPVVMR ALTQA RKVV NAIIKKYGSP VSIHIELARE LSQSFDERRK MQKEQEGNRK KNETAIRQLV EYGLTLNPTG LDIVKFKLWS EQNGKC AYS LQPIEIERLL EPGYTEVDHV IPYSRSLDDS YTNKVLVLTK ENREKGNRTP AEYLGLGSER WQQFETFVLT NKQFSKK KR DRLLRLHYDE NEENEFKNRN LNDTRYISRF LANFIREHLK FADSDDKQKV YTVNGRITAH LRSRWNFNKN REESNLHH A VDAAIVACTT PSDIARVTAF YQRREQNKEL SKKTDPQFPQ PWPHFADELQ ARLSKNPKES IKALNLGNYD NEKLESLQP VFVSRMPKRS ITGAAHQETL RRYIGIDERS GKIQTVVKKK LSEIQLDKTG HFPMYGKESD PRTYEAIRQR LLEHNNDPKK AFQEPLYKP KKNGELGPII RTIKIIDTTN QVIPLNDGKT VAYNSNIVRV DVFEKDGKYY CVPIYTIDMM KGILPNKAIE P NKPYSEWK EMTEDYTFRF SLYPNDLIRI EFPREKTIKT AVGEEIKIKD LFAYYQTIDS SNGGLSLVSH DNNFSLRSIG SR TLKRFEK YQVDVLGNIY KVRGEKRVGV ASSSHSKAGE TIRPL

UniProtKB: UNIPROTKB: A0A1W6VMQ3

-
Macromolecule #2: non-target DNA

MacromoleculeName: non-target DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Geobacillus thermodenitrificans (bacteria)
Molecular weightTheoretical: 3.615395 KDa
SequenceString:
(DA)(DT)(DA)(DC)(DA)(DC)(DC)(DA)(DA)(DG) (DC)(DT)

-
Macromolecule #3: target-strand DNA

MacromoleculeName: target-strand DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Geobacillus thermodenitrificans (bacteria)
Molecular weightTheoretical: 12.238864 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DT)(DG)(DG)(DT)(DG)(DT) (DA)(DT)(DA)(DC)(DC)(DA)(DG)(DG)(DA)(DT) (DC)(DT)(DT)(DG)(DC)(DC)(DA)(DT)(DC) (DC)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DA)(DG) (DA)

-
Macromolecule #4: single guide RNA

MacromoleculeName: single guide RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Geobacillus thermodenitrificans (bacteria)
Molecular weightTheoretical: 47.162719 KDa
SequenceString:
GGUAGGAUGG CAAGAUCCUG GUAGUCAUAG UUCCCCUGGA AACAGGGUUA CUAUGAUAAG GGCUUUCUGC CUAGGCAGAC UGACCCGUG GCGUUGGGGA UCGCCUAUCG CCCGCUUUCU UCGGGCAUUC CCCACUCUUA GGCGUUUU

-
Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8200000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63887
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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