[English] 日本語
Yorodumi
- EMDB-38239: Cryo-EM structure of Cas12j19 (E100K), crRNA and target DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38239
TitleCryo-EM structure of Cas12j19 (E100K), crRNA and target DNA complex
Map data
Sample
  • Complex: Ternary complex of Cas12J19(E100K), CrRNA and target DNA complex
    • Protein or peptide: Cas12j19(E100K)
    • RNA: CrRNA
    • DNA: TS-DNA
    • DNA: NTS-DNA
KeywordsCrispr-Cas protein / RNA BINDING PROTEIN-RNA-DNA COMPLEX
Biological speciesunclassified sequences (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXi Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Cas12j19 (E100K), crRNA and target DNA complex
Authors: Xi Z
History
DepositionDec 8, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38239.png

Downloads & links

-
Map

FileDownload / File: emd_38239.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.13281572 - 0.3202626
Average (Standard dev.)0.00005838084 (±0.007696958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_38239_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38239_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38239_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of Cas12J19(E100K), CrRNA and target DNA complex

EntireName: Ternary complex of Cas12J19(E100K), CrRNA and target DNA complex
Components
  • Complex: Ternary complex of Cas12J19(E100K), CrRNA and target DNA complex
    • Protein or peptide: Cas12j19(E100K)
    • RNA: CrRNA
    • DNA: TS-DNA
    • DNA: NTS-DNA

-
Supramolecule #1: Ternary complex of Cas12J19(E100K), CrRNA and target DNA complex

SupramoleculeName: Ternary complex of Cas12J19(E100K), CrRNA and target DNA complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unclassified sequences (unknown)

-
Macromolecule #1: Cas12j19(E100K)

MacromoleculeName: Cas12j19(E100K) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 105.573195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPSYKSSRVL VRDVPEELVD HYERSHRVAA FFMRLLLAMR REPYSLRMRD GTEREVDLDE TDDFLRSAGC EEPDAVSDDL RSFALAVLH QDNPKKRAFL KSENCVSILC LEKSASGTRY YKRPGYQLLK KAIEEEWGWD KFEASLLDER TGEVAEKFAA L SMEDWRRF ...String:
MPSYKSSRVL VRDVPEELVD HYERSHRVAA FFMRLLLAMR REPYSLRMRD GTEREVDLDE TDDFLRSAGC EEPDAVSDDL RSFALAVLH QDNPKKRAFL KSENCVSILC LEKSASGTRY YKRPGYQLLK KAIEEEWGWD KFEASLLDER TGEVAEKFAA L SMEDWRRF FAARDPDDLG RELLKTDTRE GMAAALRLRE RGVFPVSVPE HLDLDSLKAA MASAAERLKS WLACNQRAVD EK SELRKRF EEALDGVDPE KYALFEKFAA ELQQADYNVT KKLVLAVSAK FPATEPSEFK RGVEILKEDG YKPLWEDFRE LGF VYLAER KWERRRGGAA VTLCDADDSP IKVRFGLTGR GRKFVLSAAG SRFLITVKLP CGDVGLTAVP SRYFWNPSVG RTTS NSFRI EFTKRTTENR RYVGEVKEIG LVRQRGRYYF FIDYNFDPEE VSDETKVGRA FFRAPLNESR PKPKDKLTVM GIDLG INPA FAFAVCTLGE CQDGIRSPVA KMEDVSFDST GLRGGIGSQK LHREMHNLSD RCFYGARYIR LSKKLRDRGA LNDIEA RLL EEKYIPGFRI VHIEDADERR RTVGRTVKEI KQEYKRIRHQ FYLRYHTSKR DRTELISAEY FRMLFLVKNL RNLLKSW NR YHWTTGDRER RGGNPDELKS YVRYYNNLRM DTLKKLTCAI VRTAKEHGAT LVAMENIQRV DRDDEVKRRK ENSLLSLW A PGMVLERVEQ ELKNEGILAW EVDPRHTSQT SCITDEFGYR SLVAKDTFYF EQDRKIHRID ADVNAAINIA RRFLTRYRS LTQLWASLLD DGRYLVNVTR QHERAYLELQ TGAPAATLNP TAEASYELVG LSPEEEELAQ TRIKRKKREP FYRHEGVWLT REKHREQVH ELRNQVLALG NAKIPEIRT

-
Macromolecule #2: CrRNA

MacromoleculeName: CrRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 19.229471 KDa
SequenceString:
GUGCUGCUGU CUCCCAGACG GGAGGCAGAA CUGCACCUUC CAUCAGAGAA CCUCACUGCG

-
Macromolecule #3: TS-DNA

MacromoleculeName: TS-DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 13.644746 KDa
SequenceString:
(DC)(DA)(DA)(DG)(DC)(DC)(DG)(DT)(DC)(DT) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DA)(DG)(DG) (DT)(DT)(DC)(DT)(DC)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DA)(DG)(DC)(DA)(DT)(DA)(DT) (DC) (DG)(DT)(DA)(DG)

-
Macromolecule #4: NTS-DNA

MacromoleculeName: NTS-DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 13.453643 KDa
SequenceString:
(DC)(DT)(DA)(DC)(DG)(DA)(DT)(DA)(DT)(DG) (DC)(DT)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DG) (DA)(DG)(DA)(DA)(DC)(DC)(DT)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DA)(DG)(DA)(DC)(DG) (DG) (DC)(DT)(DT)(DG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104917
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