[English] 日本語
Yorodumi
- EMDB-74688: S. marcescens Cas10-Csm bound to target RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74688
TitleS. marcescens Cas10-Csm bound to target RNA
Map dataS. marcescens Cas10-Csm bound to target RNA
Sample
  • Complex: Cas10-Csm bound to target RNA
    • Protein or peptide: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
    • RNA: crRNA
    • RNA: Target RNA
    • Protein or peptide: CRISPR system Cms protein Csm2
    • Protein or peptide: CRISPR system Cms endoribonuclease Csm3
    • Protein or peptide: CRISPR system Cms protein Csm4
    • Protein or peptide: CRISPR system Cms protein Csm5
KeywordsCRISPR / crRNA / Cas10 / type III / RNA BINDING PROTEIN
Function / homology
Function and homology information


exonuclease activity / transferase activity / endonuclease activity / defense response to virus / hydrolase activity / RNA binding / ATP binding
Similarity search - Function
CRISPR-associated protein, Csm2 Type III-A / CRISPR-associated protein Csm5 / Csm2 Type III-A / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : ...CRISPR-associated protein, Csm2 Type III-A / CRISPR-associated protein Csm5 / Csm2 Type III-A / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : / Cas10/Cmr2, second palm domain / : / CRISPR type III-associated protein / RAMP superfamily / GGDEF domain profile. / GGDEF domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CRISPR system Cms protein Csm5 / CRISPR system Cms protein Csm2 / CRISPR system Cms endoribonuclease Csm3 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / CRISPR system Cms protein Csm4
Similarity search - Component
Biological speciesSerratia (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsPerdigao CC / Dokland T / Dunkle JA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142966 United States
National Institutes of Health/Office of the DirectorS10OD024978 United States
CitationJournal: To Be Published
Title: Structural insights into target detection by the S. marcescens type III CRISPR complex and its deployment in SNP identification
Authors: Perdigao CC / Ajisafe LO / Sunny AT / Wu S / Dokland T / Dunkle JA
History
DepositionDec 22, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74688.png

Downloads & links

-
Map

FileDownload / File: emd_74688.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS. marcescens Cas10-Csm bound to target RNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 420 pix.
= 394.8 Å		0.94 Å/pix.
x 420 pix.
= 394.8 Å		0.94 Å/pix.
x 420 pix.
= 394.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.13987012 - 0.32510528
Average (Standard dev.)-0.00024391853 (±0.008330687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 394.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: S. marcescens Cas10-Csm bound to target RNA, sharpened map

Fileemd_74688_additional_1.map
AnnotationS. marcescens Cas10-Csm bound to target RNA, sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: S. marcescens Cas10-Csm bound to target RNA, half map B

Fileemd_74688_half_map_1.map
AnnotationS. marcescens Cas10-Csm bound to target RNA, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: S. marcescens Cas10-Csm bound to target RNA, half map A

Fileemd_74688_half_map_2.map
AnnotationS. marcescens Cas10-Csm bound to target RNA, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cas10-Csm bound to target RNA

EntireName: Cas10-Csm bound to target RNA
Components
  • Complex: Cas10-Csm bound to target RNA
    • Protein or peptide: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
    • RNA: crRNA
    • RNA: Target RNA
    • Protein or peptide: CRISPR system Cms protein Csm2
    • Protein or peptide: CRISPR system Cms endoribonuclease Csm3
    • Protein or peptide: CRISPR system Cms protein Csm4
    • Protein or peptide: CRISPR system Cms protein Csm5

-
Supramolecule #1: Cas10-Csm bound to target RNA

SupramoleculeName: Cas10-Csm bound to target RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 340 KDa

-
Macromolecule #1: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1...

MacromoleculeName: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 90.390656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNWLAASCHV AAFALLHNLK PLAQRAGIQD FPSPALANKL FAPLPESLSA RADLHENTLT LLLDFAARLA RGLPETPVSR GETGLIPLT HLLADDNHSA PAERCYSPLA PLGVDSLMPV TAALPTGERQ AAYRQVYQAL IEGLEAIPAA HRLQPSLWLD H LDSLWMTT ...String:
MNWLAASCHV AAFALLHNLK PLAQRAGIQD FPSPALANKL FAPLPESLSA RADLHENTLT LLLDFAARLA RGLPETPVSR GETGLIPLT HLLADDNHSA PAERCYSPLA PLGVDSLMPV TAALPTGERQ AAYRQVYQAL IEGLEAIPAA HRLQPSLWLD H LDSLWMTT CHALPDGDGA SGISLYDQGK TTAALAVALW QHHARQATPE KEISLTPGDD ARLLLIQADV FGIQELIFAQ GN QTQKMAA KLLRGRSFQV SLLAETAALR VLETFDLPPV CQLINAAGKS LIVAPNLPDA AERLAGLRQR LDEWFLTHTY AQT GIGLCS TVAGSAEFLG EQAYGRLQNR LAQAMEQQKY QRFSLCAGDA PPPVFEGYLD QIAQGAGGEP CPMNGLHPVE TTLN GLGCS RLAADQITLG HWINHGHWIS HGERYARLLI LRDSTATFSD DRCLHLTLFG YQVVAVSLKE DSGEFGELAC NGSLR RCWD VSLPPEGTSL FQGYARRFIN GWMPLAQGEY QPECYPGIEE ALANGDIKTF DHLSCEDLYQ DADQSLRGTC ALGVLK GDI DNLGHLFRSG LPQPGFAKTI GLSRQIHLFF TLWLPHLCRK DPRFANTYTV FAGGDDFFLI GPWRSQQTLA LTMAQDF AR YSGHNPALHF SLGLVQAKPG YPVRALAAQA EAALKQAKQH PGKNAICLYN EVMGWPEYDA LLACSEELAR WREHDGYP L SSGLLYRLLA LSEQSAEESE KPQAALWRSR LAYFLRRNLV DNVKVPTKEN PAAFRHQLHL ELFEKLEQHL KRHRQRYRV ALQRHLYHYR TVPRGE

UniProtKB: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)

-
Macromolecule #4: CRISPR system Cms protein Csm2

MacromoleculeName: CRISPR system Cms protein Csm2 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 15.886099 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHTTL DYFKRQLHKP EATFFDDDAQ KFAEQLAQYG KKGKPTQLRR FYDQLQQLEQ RINGDEEKLA LYLPEIRMIS AHLAYAKGR ELISDEFCQT MQNLIRSINT CQHLKNGRLF FEATLGFLRA IRRD

UniProtKB: CRISPR system Cms protein Csm2

-
Macromolecule #5: CRISPR system Cms endoribonuclease Csm3

MacromoleculeName: CRISPR system Cms endoribonuclease Csm3 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 27.185859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLNNIQTLR ATLVCETGLH IGGGDTALQI GGIASAVVRH PLTQQPYIPG SSLKGKLRSL LEWRAGVVGD TEGKVLSHQV YQQLIDDKK QAQALQALKI LQLFGVSGGD KLSAEQAQQI GPTRLSFWDC EFDEHWLAQQ GGRVQTEEKA ENCIDRISGV A LHPRFIER ...String:
MQLNNIQTLR ATLVCETGLH IGGGDTALQI GGIASAVVRH PLTQQPYIPG SSLKGKLRSL LEWRAGVVGD TEGKVLSHQV YQQLIDDKK QAQALQALKI LQLFGVSGGD KLSAEQAQQI GPTRLSFWDC EFDEHWLAQQ GGRVQTEEKA ENCIDRISGV A LHPRFIER VPAGSRFDFR LTVRQLDGDS PDLLDTLLAG LKMLELDGLG GSISRGYGKV RFEALTLDGK DLQPRFEQLQ PF KHTTQGA G

UniProtKB: CRISPR system Cms endoribonuclease Csm3

-
Macromolecule #6: CRISPR system Cms protein Csm4

MacromoleculeName: CRISPR system Cms protein Csm4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 35.770551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPSPVAPAAA WQWLRLRLLP DSAFATALRG DTLFGQLCWY LRESLGEAGL NALLAGYHDQ RPFAVISDPM LADHLPRPHL PEHRLGFAA ADARARKQRK QQCWLPLAFA HQPLAEWGAH LTAAPEHHQH RSDVQMHNSI NRQTLTTGGD DAFAPFGSEQ H WFDVDTAW ...String:
MPSPVAPAAA WQWLRLRLLP DSAFATALRG DTLFGQLCWY LRESLGEAGL NALLAGYHDQ RPFAVISDPM LADHLPRPHL PEHRLGFAA ADARARKQRK QQCWLPLAFA HQPLAEWGAH LTAAPEHHQH RSDVQMHNSI NRQTLTTGGD DAFAPFGSEQ H WFDVDTAW DLYLLHDKRL SAAQLTDALR AIGLLGYGKD ASIGKGRFHL TPQPMPELPT PDGNPLRLTL APCAPQQGHW HS ADSFFSP LVRVGRHGAA LVVQGHPFKN PLLLADSAAV LAPVTPDNRP FVGQGLGGNG RLSTALPQTV HQGYAPVIPV RFH HKAQPQ

UniProtKB: CRISPR system Cms protein Csm4

-
Macromolecule #7: CRISPR system Cms protein Csm5

MacromoleculeName: CRISPR system Cms protein Csm5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 63.148707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRDQTPRRH TACDSDNMQY FTLTCLSPVH VATGDSLNPG EYLIDENALY ELGQGGLSPA LTATQRSELL TILESNDPAL PLTVQRFLA REAGKLKYAA RRMCPLLPGI SRYYQSRLGQ VMQNDTKNKK QMINQLELMR HVGAALGAPY IPGSTLKGAI R TALVSALN ...String:
MTRDQTPRRH TACDSDNMQY FTLTCLSPVH VATGDSLNPG EYLIDENALY ELGQGGLSPA LTATQRSELL TILESNDPAL PLTVQRFLA REAGKLKYAA RRMCPLLPGI SRYYQSRLGQ VMQNDTKNKK QMINQLELMR HVGAALGAPY IPGSTLKGAI R TALVSALN QGQPLQAERR ETDKLSSKVA QDAERQLLGF DTRRDSPRYR IEHDPFHWLQ VGDAVSPAEH PPMLDYWLVR RQ PFKRTEK QDNKADNMEL SPVECLKPRQ SPLHCQITVK TPPTALAIKN PRLKQWLGKV SQLAQQVNRI TLPQCHHELA WLA EKHIGT DDVYAPGQNW VAQMQQLLRQ LDDPLQRGEA LLLRVGKYGG AISKTVAGWR HIARLGRQGT RTTYHPDVTT CTLA LPQAD ALTQALPFGW VLLHQPDQPE VTEFVASHHD WCQQQQQRLD AHQQQQHTHR QQRQQLAQAR EEEAQRLADK ARQSK ARQS IMSLAEQLAS EQTFQHKNPN GPLRGQLATC VGCVATEGSA EEKAELCTLF DDILNYWGIK PGKDKKLTAL RNKLL

UniProtKB: CRISPR system Cms protein Csm5

-
Macromolecule #2: crRNA

MacromoleculeName: crRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 13.361948 KDa
SequenceString:
AUUAAGACCA UUUACAGAAC CUGUUCCACU UAAUGAAGUU GC

-
Macromolecule #3: Target RNA

MacromoleculeName: Target RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 13.560099 KDa
SequenceString:
GCAACUUCAU UAAGUGGAAC AGGUUCUGUA AAUGCGGAAG UA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.1 µm

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 129762
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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