[English] 日本語
Yorodumi
- EMDB-75686: Effector complex from type IV-C CRISPR-Cas system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75686
TitleEffector complex from type IV-C CRISPR-Cas system
Map data
Sample
  • Complex: Effector complex from type IV-C CRISPR-Cas system
    • Protein or peptide: Cas7c
    • Protein or peptide: Cas5c
    • Protein or peptide: Cas11c
    • DNA: Target Strand DNA
    • RNA: crRNA (47-MER)
    • Protein or peptide: Cas10IVc
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsCRISPR-Cas / nuclease / RNA-guided / Cas10 / Cas7 / RNA BINDING PROTEIN
Biological speciesPyrococcus abyssi (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsPittman C / Xu C / Catchpole R / Garrett S / Fuchs R / Makarova K / Koonin E / Zhao P / Wells L / Graveley B ...Pittman C / Xu C / Catchpole R / Garrett S / Fuchs R / Makarova K / Koonin E / Zhao P / Wells L / Graveley B / Chu X / Ke A / Terns M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35118174 United States
CitationJournal: To Be Published
Title: Type IV-C CRISPR-Cas effector complex recognizes double-stranded DNA and switches on collateral cleavage of ssDNA and RNA
Authors: Pittman C / Xu C / Catchpole R / Garrett S / Fuchs R / Makarova K / Koonin E / Zhao P / Wells L / Graveley B / Ke A / Terns M
History
DepositionFeb 23, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75686.png

Downloads & links

-
Map

FileDownload / File: emd_75686.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.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.36617726 - 0.92401385
Average (Standard dev.)0.00029486942 (±0.0222109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_75686_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_75686_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Effector complex from type IV-C CRISPR-Cas system

EntireName: Effector complex from type IV-C CRISPR-Cas system
Components
  • Complex: Effector complex from type IV-C CRISPR-Cas system
    • Protein or peptide: Cas7c
    • Protein or peptide: Cas5c
    • Protein or peptide: Cas11c
    • DNA: Target Strand DNA
    • RNA: crRNA (47-MER)
    • Protein or peptide: Cas10IVc
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Effector complex from type IV-C CRISPR-Cas system

SupramoleculeName: Effector complex from type IV-C CRISPR-Cas system / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Pyrococcus abyssi (archaea)

-
Macromolecule #1: Cas7c

MacromoleculeName: Cas7c / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 36.531379 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRVVLKIKAL EPISVGYESI GIETLLYSLP IIKEDGTALE VPVIPGNSLR GVLRDKMALQ FLEDVKSVLI GSKQGSLEAH IGTLLSLFS GGILSGKEKD QSTPNIKEIM EKYVYPLLPL SIMGVALKKI IIPGKIKVGI GYPVTKETKS LLTDLGVPFD E SAPTLSEI ...String:
MRVVLKIKAL EPISVGYESI GIETLLYSLP IIKEDGTALE VPVIPGNSLR GVLRDKMALQ FLEDVKSVLI GSKQGSLEAH IGTLLSLFS GGILSGKEKD QSTPNIKEIM EKYVYPLLPL SIMGVALKKI IIPGKIKVGI GYPVTKETKS LLTDLGVPFD E SAPTLSEI ISSVLITRKD DMNKVMQLKE LLNVQGKVEE VKAGDSAVQQ RLYRQVVVPG TVFYSYVEDI IPMTEAEWGL VL KTLEHLD KIGGRVAGGL GKVKIELHGI NKERKENFIH AYENYIRDNI TDIQEALKKS PNDFFRGSSK SRENVEIDEK AQG RKEPKD SPEA

-
Macromolecule #2: Cas5c

MacromoleculeName: Cas5c / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 35.403852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYLVTLRFRT YPLFLSLSNP NELSQELTPL DGPLAFAEYY RTRLSNDPDW RVKYLEDILT ARKLEWISDI RSSYLLPCTV NKETLTITT PMGFKAVFNV DEKKEAHYKF SEGQPLKKWE SSQIFLRLGR RDDIIKVEIL RNSLGVRLTK KTKGLPSSHS G SYKAVDYS ...String:
MYLVTLRFRT YPLFLSLSNP NELSQELTPL DGPLAFAEYY RTRLSNDPDW RVKYLEDILT ARKLEWISDI RSSYLLPCTV NKETLTITT PMGFKAVFNV DEKKEAHYKF SEGQPLKKWE SSQIFLRLGR RDDIIKVEIL RNSLGVRLTK KTKGLPSSHS G SYKAVDYS LRLYTPNLMW ASVVNGISQR KLDELLRILG KFGIGKKRNM GWGDLLDYQI YELKGENITP DYILHKRGES RF LETWRPI SPEKIAEMIT KSPKGVKLYL LDSKIGYGAD RPPYWRRNLV VKSALFLVQN NNGTTGNVS

-
Macromolecule #3: Cas11c

MacromoleculeName: Cas11c / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 14.065316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIYKKEVAPV QEKEKIEDLV VSLLGAIDGI IDWGSMGEKV HRKKYSILAK RIAVVAKSSN SLDEFVEKLL SQVAGDSLFI SREKGENFK EVYRKAKEHE GEVLKFLKAY PYLSTVLYAA YVESI

-
Macromolecule #6: Cas10IVc

MacromoleculeName: Cas10IVc / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 70.278211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEIGREKTL NEFITIKRNS RKSKDKSTIS PRIQKVQMLS QESSFALIKG TIARTDPASG LPHLDELTHH LIAVSSASLK FSSGEIALA ALIHDYYKPV FDFRWNTQKN RWEWYHYITD QKTYSQLLSE FNDSINVSKV ASISKEHHKK GKCNEICQIE Q KSKLISAL ...String:
MKEIGREKTL NEFITIKRNS RKSKDKSTIS PRIQKVQMLS QESSFALIKG TIARTDPASG LPHLDELTHH LIAVSSASLK FSSGEIALA ALIHDYYKPV FDFRWNTQKN RWEWYHYITD QKTYSQLLSE FNDSINVSKV ASISKEHHKK GKCNEICQIE Q KSKLISAL ETSLPFTLPQ RDNYVIVQHL RVPGKYRMFL LALLKEMLSK ELSSRYSKRF QEILGISRIR YEYRPISDLE RT GDKRIED VERIIQKNDW KIEIKENTMI IPLPSKFHKE VFYFEYYEGS EIVLDIDTKA RMIRGVKVPF GMALSTVYFA GAQ DAYLVY VDAGNGLLPL DTLLGTLIED LKRSLSKDKQ ETAFNSIDIS KIVRSLTGKF KSDAMCVFCG EPGEPISNNE KVKR IMEDK FTDTWLLLTH GASVCPACKL GFEIEELFRA KGMNKYLAEE AILKMHLIST DVPIFRSENF LRSISSKIWL ELLSE VYYS LHRSKELQKI TKKNEWATAF YLNPKVIIYP YIADMTPQVL SVTLRYSNKK FVLQSGIHSR VVFPGEEKDM TFEEFR IVR KFYSSHPTTG SNLVKRIRSV YNPIFGVPKV DIQKGGGSRA RKRKN

-
Macromolecule #4: Target Strand DNA

MacromoleculeName: Target Strand DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 11.444326 KDa
SequenceString:
(DT)(DT)(DG)(DT)(DA)(DG)(DT)(DA)(DT)(DG) (DC)(DG)(DG)(DT)(DC)(DC)(DT)(DT)(DG)(DC) (DG)(DG)(DC)(DT)(DG)(DA)(DG)(DA)(DG) (DC)(DA)(DC)(DT)(DT)(DC)(DA)(DG)

-
Macromolecule #5: crRNA (47-MER)

MacromoleculeName: crRNA (47-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 15.131104 KDa
SequenceString:
AUUGAAAGCU GAAGUGCUCU CAGCCGCAAG GACCGCAUAC UACAAGA

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS 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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 883889
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38895
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