[English] 日本語
Yorodumi
- EMDB-0641: Cryo-EM structure of Csm-crRNA-target RNA ternary complex in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0641
TitleCryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas system
Map data
Sample
  • Complex: Csm-crRNA-target RNA-AMPPNP complex
    • Protein or peptide: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
    • Protein or peptide: Csm2
    • Protein or peptide: Csm3
    • Protein or peptide: Csm4
    • RNA: RNA (38-MER)
    • RNA: RNA (40-MER)
    • Protein or peptide: Csm5
    • RNA: Cyclic DNA cA4
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-MONOPHOSPHATE
Keywordscryo-EM structure / Csm-crRNA-target RNA ternary complex in complex with CA4 / Type III CRISPR-Cas systerm / IMMUNE SYSTEM / immune system-rna-dna complex / immune system-rna complex
Function / homology
Function and homology information


exonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / ATP binding / identical protein binding
Similarity search - Function
CRISPR-associated protein Csm5 / CRISPR-associated protein, Csm2 Type III-A / 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-associated protein Csm5 / CRISPR-associated protein, Csm2 Type III-A / 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 / HD domain profile. / GGDEF domain profile. / GGDEF domain / HD domain / HD domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / CRISPR system Cms protein Csm2 / CRISPR system Cms endoribonuclease Csm3 / CRISPR system Cms protein Csm4 / CRISPR system Cms protein Csm5
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea) / Thermococcus onnurineus (strain NA1) (archaea) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJia N / Patel DJ
CitationJournal: Mol Cell / Year: 2019
Title: Second Messenger cA Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path.
Authors: Ning Jia / Roger Jones / George Sukenick / Dinshaw J Patel /
Abstract: Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA) formation from ATP subunits positioned within the composite pair ...Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cA) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit. The generated cA second messenger in turn targets the CARF domain of trans-acting RNase Csm6, triggering its HEPN domain-based RNase activity. We have undertaken cryo-EM studies on multi-subunit Thermococcus onnurineus Csm effector ternary complexes, as well as X-ray studies on Csm1-Csm4 cassette, both bound to substrate (AMPPNP), intermediates (pppA), and products (cA), to decipher mechanistic aspects of cA formation and release. A network of intermolecular hydrogen bond alignments accounts for the observed adenosine specificity, with ligand positioning dictating formation of linear pppA intermediates and subsequent cA formation by cyclization. We combine our structural results with published functional studies to highlight mechanistic insights into the role of the Csm effector complex in mediating the cA signaling pathway.
History
DepositionMar 7, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseJul 31, 2019-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o7h
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0641.png

Downloads & links

-
Map

FileDownload / File: emd_0641.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.)
1.09 Å/pix.
x 256 pix.
= 278.784 Å		1.09 Å/pix.
x 256 pix.
= 278.784 Å		1.09 Å/pix.
x 256 pix.
= 278.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.089 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.16710114 - 0.3501203
Average (Standard dev.)0.00017349591 (±0.005167198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.784 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0891.0891.089
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z278.784278.784278.784
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1670.3500.000

-
Supplemental data

-
Sample components

+
Entire : Csm-crRNA-target RNA-AMPPNP complex

EntireName: Csm-crRNA-target RNA-AMPPNP complex
Components
  • Complex: Csm-crRNA-target RNA-AMPPNP complex
    • Protein or peptide: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
    • Protein or peptide: Csm2
    • Protein or peptide: Csm3
    • Protein or peptide: Csm4
    • RNA: RNA (38-MER)
    • RNA: RNA (40-MER)
    • Protein or peptide: Csm5
    • RNA: Cyclic DNA cA4
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-MONOPHOSPHATE

+
Supramolecule #1: Csm-crRNA-target RNA-AMPPNP complex

SupramoleculeName: Csm-crRNA-target RNA-AMPPNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Thermococcus onnurineus (archaea)

+
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 / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 89.750602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPMEIDEL TALGGLLHDI GKPVQRAGLY SGDHSTQGAR FLRDLAENTG RAEYELLSLF SEFHHKGHMK NDELMIRRI KELSPERFGL TMEDVLNALW IVYEADNLAS GEREEGQPQA SRPLYSVFNP GKAYPWAELD FEKELPVPGD V FSIRSQDY ...String:
MGSSHHHHHH SQDPMEIDEL TALGGLLHDI GKPVQRAGLY SGDHSTQGAR FLRDLAENTG RAEYELLSLF SEFHHKGHMK NDELMIRRI KELSPERFGL TMEDVLNALW IVYEADNLAS GEREEGQPQA SRPLYSVFNP GKAYPWAELD FEKELPVPGD V FSIRSQDY RELVKRLWEE LSKAKLRSDR LLPVLEKYLT FVSSVTSEGN IISLYDHMRM TSAIALAMLR AGCTAEDVRS GR CRKEKRF LLIEGDFSGI QDFIYRVSGK GTLKYLRARS AYLELIGWDV VLEILSRLGL TRANVVFNAG GHFMIIAQNT PDA VKELEE IRAKAVEWLY REFESDLYLA IEWEPVSGRE FGREGGKNLF AEARKRLKHK LTVRKLKRFG EIKGLFEHGH TERL AECPV CGRELPEGKL EPSASDPETK VCPTCNRLVS LGGNLPKLLG FGRTAKNDAG VLVEGPFSGF VPYLQGGRPV GEQIL VKNT LNPGEIPESA QFVPYFVADY FKKDPKGGVA TFEELSMAST GTRRLGVMKG DVDRLGEFFS SMDSPSKLAT ASRFMD YFF KGYIGAIIEG KFGYIIGDVP SLRDWPEEPD IVVVYAGGDD FFIVGAWDQI FELAFRVRRA FNAYTGGKLT LSVGLGY FD ERTPIYRMAD VVSERLDTAK DEGRNRVFVV GRSRPLDGKH KLSYEWNHYE ELWRTYAPRI YAGNGRLKGK LESKKGLL W KLLEIRELYV RDPNDVRWAY LTAYLLGRHG LSDLFPELVG IDTKAVERKE PQPVYWVDGV LKIVLMAVRR

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

+
Macromolecule #2: Csm2

MacromoleculeName: Csm2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 21.235279 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSVAYHQKHG GYGRGGYGRQ DRPQVDASRL FGESPDVVGI KKMLEGKGKQ WEAIQPYFDN VVREAKNFLE WSPNKRLANA VTVAAYLTS QGLKTNQVRK ILDMARTTEL KVKRGEGDIK DDLVKMRYLL AYTVGKATGQ SKYSLDAFHR ILDPMLEVLM G SPKKENFE KFYDFLQAVV AYHKFFGGGD

UniProtKB: CRISPR system Cms protein Csm2

+
Macromolecule #3: Csm3

MacromoleculeName: Csm3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 32.822051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMDRRFYGK IVIKGKIKAV TGLHIGSQRD ISEIGGIANP VIKDPHTGLP YIPGSSLKGR LRSLFEILVN SRLGEWREKY PSLANYSPG SCRPDNQENC GKFFNRKINR GWIHVCPDYE TALACPVCRL FGASGKESNF PSRIIVRDAF LTKEWEEKWR A GEAITEAK ...String:
GSMDRRFYGK IVIKGKIKAV TGLHIGSQRD ISEIGGIANP VIKDPHTGLP YIPGSSLKGR LRSLFEILVN SRLGEWREKY PSLANYSPG SCRPDNQENC GKFFNRKINR GWIHVCPDYE TALACPVCRL FGASGKESNF PSRIIVRDAF LTKEWEEKWR A GEAITEAK IEVGIDRVTS QANPRTNERV VAGAEFEFEI IYNVENTTHW RDDIKNLLTA MALLEDSYLG GSGSRGYGKV KF IFDSFEF RPLDYYRTGK DEDIVSIDAR EKSVSDILSG FDSLFSEVEG KLEAG

UniProtKB: CRISPR system Cms endoribonuclease Csm3

+
Macromolecule #4: Csm4

MacromoleculeName: Csm4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 32.345061 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPKFIAVKLI PKGPFRDIPR ADTLFGAIGN AISAIHGQSA VEELVDAFVG GARISSAFPY SGDTYYLPKP LSVEPALEGI LTGLDEEER YTTAKRLRKA KYLDLKNFEL ALRLRPFTIP EEIPYARVDV PRVVLDRVTQ DSSIYFWEEI RFREKSGVYF L YSGPREVF ...String:
MPKFIAVKLI PKGPFRDIPR ADTLFGAIGN AISAIHGQSA VEELVDAFVG GARISSAFPY SGDTYYLPKP LSVEPALEGI LTGLDEEER YTTAKRLRKA KYLDLKNFEL ALRLRPFTIP EEIPYARVDV PRVVLDRVTQ DSSIYFWEEI RFREKSGVYF L YSGPREVF DGYIAPAMRF LGDTGIGGKS TWGAGLFEVE FHEMKIDAPG SEYSVTLSNA LPTKTPVLWR LLRKGGWSFG RR KPRMTFI AEGSIVKNDP GGMERLELGL SHEVYVYGLT FPLGVELPEG LE

UniProtKB: CRISPR system Cms protein Csm4

+
Macromolecule #7: Csm5

MacromoleculeName: Csm5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Molecular weightTheoretical: 40.58841 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTERTLKVLS PLHIGTGNEL TPVDIYPREN IIHVLDTER(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
MTERTLKVLS PLHIGTGNEL TPVDIYPREN IIHVLDTER(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)RKSMQIKEF IKLNGRPYIP GSSLKGAIRT AVLYKA LKE C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)IRY EPKRDPMKAL IV RDSKPVG RKHLAVYHVE VIGNPQPIPI WVEAIEPGAA TDVEIHVDTE ALRLNADYFN GLLWECLKER GEPGEVFEDF LWE AVDEFY TAVMKYETIE VQKFGRYTSQ VRSFYASLED HSGHVLRLGW GSGWLAMTIG LLLVEKGYKW ENVRKKLGLG KKPG GSGFS REFPKTRRLA DGMPMGWVVL EHHHHHH

+
Macromolecule #5: RNA (38-MER)

MacromoleculeName: RNA (38-MER) / type: rna / ID: 5 / Details: crRNA / Number of copies: 1
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea)
Molecular weightTheoretical: 12.463438 KDa
SequenceString:
GUGGAAAGGC GGGCAGAGGC GGUUUGCGUA UUGGGCGC

+
Macromolecule #6: RNA (40-MER)

MacromoleculeName: RNA (40-MER) / type: rna / ID: 6 / Details: taget RNA / Number of copies: 1
Source (natural)Organism: Thermococcus onnurineus (strain NA1) (archaea)
Molecular weightTheoretical: 12.750658 KDa
SequenceString:
CCCUGGCGCC CAAUACGCAA ACCGCCUCUG CCCGCGGGCG

+
Macromolecule #8: Cyclic DNA cA4

MacromoleculeName: Cyclic DNA cA4 / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.271866 KDa
SequenceString:
AAAA

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #10: GUANOSINE-5'-MONOPHOSPHATE

MacromoleculeName: GUANOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: 5GP
Molecular weightTheoretical: 363.221 Da
Chemical component information

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151715
Initial angle assignmentType: RANDOM ASSIGNMENT
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