[English] 日本語
Yorodumi
- EMDB-66346: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66346
TitleCryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state
Map data
Sample
  • Complex: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state
    • Complex: RNA
      • RNA: CRISPR RNA
      • RNA: Cognate target RNA (CTR)
    • Complex: Cas7x3-Cas7-5-Cas10
      • Protein or peptide: Cas10
      • Protein or peptide: CRISPR type III-associated protein domain-containing protein
      • Protein or peptide: TIGR03986 family CRISPR-associated RAMP protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: ZINC ION
  • Ligand: water
KeywordsCRISPR / Anti-phage defense / Second messenger / SAM-AMP / IMMUNE SYSTEM
Function / homology: / : / :
Function and homology information
Biological speciesGammaproteobacteria bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMitsuda Y / Ishikawa J / Nagahata N / Hiraizumi M / Yamashita K / Nishimasu H
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
Japan Society for the Promotion of Science (JSPS)25H00436 Japan
CitationJournal: To Be Published
Title: Structural mechanism of SAM-AMP synthesis by the type III-D2 CRISPR effector complex
Authors: Mitsuda Y / Sugaya M / Ishikawa J / Nagahata N / Okazaki S / Hiraizumi M / Kato K / Gootenberg JS / Abudayyeh OO / Osawa T / Yamashita K / Nishimasu H
History
DepositionSep 25, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_66346.png

Downloads & links

-
Map

FileDownload / File: emd_66346.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.)
1 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.84883296 - 1.5313027
Average (Standard dev.)-0.000061022678 (±0.030045362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_66346_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66346_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66346_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex ...

EntireName: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state
Components
  • Complex: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state
    • Complex: RNA
      • RNA: CRISPR RNA
      • RNA: Cognate target RNA (CTR)
    • Complex: Cas7x3-Cas7-5-Cas10
      • Protein or peptide: Cas10
      • Protein or peptide: CRISPR type III-associated protein domain-containing protein
      • Protein or peptide: TIGR03986 family CRISPR-associated RAMP protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: ZINC ION
  • Ligand: water

+
Supramolecule #1: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex ...

SupramoleculeName: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Gammaproteobacteria bacterium (bacteria)

+
Supramolecule #2: RNA

SupramoleculeName: RNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #5

+
Supramolecule #3: Cas7x3-Cas7-5-Cas10

SupramoleculeName: Cas7x3-Cas7-5-Cas10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4

+
Macromolecule #1: CRISPR RNA

MacromoleculeName: CRISPR RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Gammaproteobacteria bacterium (bacteria)
Molecular weightTheoretical: 13.71808 KDa
SequenceString:
AUUGAAACUU GUCUUCGACA UGGGUAAUCC UCAUGUUUGA AUG

+
Macromolecule #5: Cognate target RNA (CTR)

MacromoleculeName: Cognate target RNA (CTR) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Gammaproteobacteria bacterium (bacteria)
Molecular weightTheoretical: 15.180135 KDa
SequenceString:
GGCAUUCAAA CAUGAGGAUU ACCCAUGUCG AAGACAACAA AGUUAGG

+
Macromolecule #2: Cas10

MacromoleculeName: Cas10 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gammaproteobacteria bacterium (bacteria)
Molecular weightTheoretical: 67.985797 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MNYYLRVEGV NLGSFVNDTN DLATIRGGSL LLLEAMEDIV EKILGKHSSS LSARESFDQL LDKRNVLSA RIKEAKKKQD HALRKKLEQE VRDIKSQIKH LKGKISCRGK GGSSCRETIS KGASWGLFEL DVDESTAAKI K QGLIGAFN ...String:
MGSSHHHHHH SSGLVPRGSH MNYYLRVEGV NLGSFVNDTN DLATIRGGSL LLLEAMEDIV EKILGKHSSS LSARESFDQL LDKRNVLSA RIKEAKKKQD HALRKKLEQE VRDIKSQIKH LKGKISCRGK GGSSCRETIS KGASWGLFEL DVDESTAAKI K QGLIGAFN DDPKYKYATF VVDLYRPEDG EGYRSRRDKV QTLNRYQQLK TLSLAITNQG KDVCTLNKVT PANDERDLPA NS GEKNRDY ISDSVYQRRE YGRGQNVYTG FYKKNTGIDG VKPTKDLEQL SSDAPYPALE GKIAYIYIDG NKFGQKQKEA DSV TEQRSF DQQTREGRKE VLAGILEQIK EDPDWRCGER LRLETLLWGG DEIIWVVPAW RGWWMLKRFY ELAREQIRLV TKDK NGQDE ITRLFHGSSI IFCKHNAPIH RINTLARSLA DGFAKIENFK KRNMIAYQVL ESFDHAGTNL RDYRKNQLKG LSDKL PDFL VEAEQMEAIE DSISKLKQME FPKRKIYQIV QQYRVGMPDE AEKLRKKITG GDYSELTPEQ KEECDKIATE LEHLKS IFG GSNAYWLHLM ELWDYVSPER VDAELQEGE

UniProtKB: UNIPROTKB: A0A9D0P2E0

+
Macromolecule #3: CRISPR type III-associated protein domain-containing protein

MacromoleculeName: CRISPR type III-associated protein domain-containing protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gammaproteobacteria bacterium (bacteria)
Molecular weightTheoretical: 70.690969 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MQKATLKIGL TLKGPLITQA SDPGDLGLDM VVATHQDGAH YLPGTLIVGK LRQALEELKE VVSLRGGGPM TDWFKPDLDT WLGRPSQTG LPNTKQLYFS DFDLDAESSS KMRSGLVRDR ITIEAETGAV KPRHIVMIEN PFVSGEEYTF TGTLHFFTTE A ATILKHIK ...String:
MQKATLKIGL TLKGPLITQA SDPGDLGLDM VVATHQDGAH YLPGTLIVGK LRQALEELKE VVSLRGGGPM TDWFKPDLDT WLGRPSQTG LPNTKQLYFS DFDLDAESSS KMRSGLVRDR ITIEAETGAV KPRHIVMIEN PFVSGEEYTF TGTLHFFTTE A ATILKHIK TGFNWFSQVG AMKSVGFGQV VGVGFGEPTY ATITPPASAP PAVTTPYVDL VIKPIYPFCI TGRSLSDNLF ES AAIIPGG AIIGSIATTW SHLVGQHDGR IGDDPERKQL KENFSKLRIT HAFPSTADNK RPVVAPLSLV TIDGDQKTYY DVA RLEAPC LINGQPPDFA LDWKDNEDTL KEYPWPFIRM KEWGWASLSA ELRVRTAIDR DYHRSKKSQL FAYEQVVPSG KAWY SRLDL SRIADDYTRS AVLEQLRTLV EQGVYGLGKT KTPFELELLP ADTVTPMVQS SSDPVAGRLW IVTLQTDTLL GSPEP LDET SGECELEIMY SKAWCELSNG NLRLLRYFAR QKQAGGRYLK EVFQKGHSSY RPWLLTEAGS VFVLEADGDD MEEAQR LIK EWLQQGLPLT NEVRKYYRIE SSRVTWEQCP FLAQNGYGEI AVNLEMDGLA TVLPDDSCNI TPIKRTTTGE EG

UniProtKB: UNIPROTKB: A0A9D0P213

+
Macromolecule #4: TIGR03986 family CRISPR-associated RAMP protein

MacromoleculeName: TIGR03986 family CRISPR-associated RAMP protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gammaproteobacteria bacterium (bacteria)
Molecular weightTheoretical: 138.380078 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SMTTVKEKSW AFTGLKRWKI ITTLETQTPL HIGSGEVAEI EINDSQGDRR QVQANAIIRG KDDKPIIPGS TLKGKLRSHF ESCLDHSKA LERVFGKEYQ SDEEQGRGGL AEFHDAVCSY VAPGNSYYPN WNEARNTYIE ASTTIDCHTG TAADATLHYN E CVPPGTRF ...String:
SMTTVKEKSW AFTGLKRWKI ITTLETQTPL HIGSGEVAEI EINDSQGDRR QVQANAIIRG KDDKPIIPGS TLKGKLRSHF ESCLDHSKA LERVFGKEYQ SDEEQGRGGL AEFHDAVCSY VAPGNSYYPN WNEARNTYIE ASTTIDCHTG TAADATLHYN E CVPPGTRF LVTVTGAMSD KDAALIVAAL QAFGDETNPI HLGAEEANGK GRMGLFGNVE VSCLDHDDII AWISQGSDAR MA TDKFKPL GKEKVNDLAK NITTPTATGG AQRQHFGIEL KFDGPFLVND PSKYSKGDGD QPAVHQPLTD RSNNPILPAR SFR GAIRAQ AERIIRTMGG ACCDTQSPCQ NSGQLCIACQ MFGTTGWKTT LSISDFTYDG EYRPAKTQQF VAIDRFHGGG KDGA LFSIK YFERPVLKGG ISLKLRNQNA DELSWRKGLL ALLFRDLQEG DITFGFGANK GYGGVEEACI TNADVISTAD IEAFR AKCH ANHADSWCSP VSKPTNRDDK SSLPSINPAT GAGHAFHNPY HFIPIKAPDT STWLDKHKLA TPGSPHSHAY YRSCSD DDK PLHHGRITCK LTAETPLFVG SGDAENQLTD SEAKLKEHYQ LNNKLAIPAT SLRGLISSLA EAASNSALRV LDNGVLS YR KPASRALRKI GILFKREEQW RLVQMEGNLA NAIKLKSAYT NQKMMDFLAN KQSWSPEHNV VYYLSADFRP GDVPQETY L AGRICGILRI LGGKDGDRKN ELENKKHELF IRVDEQYVDT EINRFDYEEY VRQGGIPVSP SAVERYTELA DQRSLSQKN SRDLKGDNNC CSDKWLPFHL KGAARYKKEK ACLLPLREYD LVYFDSDGTQ VTEISFSAIW RDRVADKVHA FFPEELRPFN QKRKWISPA ELLFGFVELN DNKDERDHAQ AFTGKVRVAA GVLSPDDSIR QGDLQEHEPI MLKALSSPKL PSPALYFKQK S GDHRYIAK PDLKKASHQA QGRKIYLHAL RDQKDDVQKL NTKGQPANGN GAHLPWKTAD EDERPQLKVR IRPLKPGTSF YF HLDYNNL TEWELGLLCY VLQPSETFRH KLGMGKPIGL GTVKIEIATL QTIDRQKRYR EAGANEHRHN GSNWVNESLR DEL ERLPGT VELSPDRQPE AKLRPDELRQ SFIATMDNDI YRAIELLGDP HNIKYPVHYP QVRNKSIEQE NFKWFVANDS GSGD QRKGT GIDAKEEPMR SIDQISTTIP TLNRYEWNGD

UniProtKB: UNIPROTKB: A0A9D0P2B2

+
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #7: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

+
Macromolecule #8: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 17 / 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

Concentration0.15 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H17N2O4SNaHEPES-NaOH
5.0 mMMgCl2magnesium chloride
1.0 mMC15H22N6O5SS-adenosylmethinonine
1.0 mMC10H17N6O12P3Adenylyl imidodiphosphate
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.833 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 371927
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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