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- EMDB-43796: Structure of the guideless DtCmr Type III CRISPR complex -

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Basic information

Entry
Database: EMDB / ID: EMD-43796
TitleStructure of the guideless DtCmr Type III CRISPR complex
Map dataSharpened map
Sample
  • Complex: Guideless type III CRISPR complex from Dissulfurispira thermophila
    • Protein or peptide: CSD domain-containing protein Cmr6
    • Protein or peptide: Type III-B CRISPR-associated protein Cas10/Cmr2
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR type III-B/RAMP module-associated protein Cmr5
    • Protein or peptide: Type III-B CRISPR module-associated protein Cmr3
  • Ligand: ZINC ION
KeywordsCRISPR / complex / guideless / IMMUNE SYSTEM
Function / homology
Function and homology information


defense response to virus / nucleic acid binding / cytoplasm
Similarity search - Function
CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal ...CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / : / Cas10/Cmr2, second palm domain / Cold shock domain / Cold shock protein domain / CRISPR type III-associated protein / RAMP superfamily / GGDEF domain profile. / GGDEF domain / Reverse transcriptase/Diguanylate cyclase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Type III-B CRISPR module-associated protein Cmr3 / CSD domain-containing protein / CRISPR type III-B/RAMP module-associated protein Cmr5 / Type III-B CRISPR module RAMP protein Cmr4 / Type III-B CRISPR-associated protein Cas10/Cmr2
Similarity search - Component
Biological speciesDissulfurispira thermophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBurman N / Henriques WH / Pandey S / Wiedenheft B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134867-01 United States
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionFeb 23, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_43796.map.gz / Format: CCP4 / Size: 73.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.13 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0028607463 - 2.0755112
Average (Standard dev.)0.002465624 (±0.037203223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions268268268
Spacing268268268
CellA=B=C: 302.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Guideless type III CRISPR complex from Dissulfurispira thermophila

EntireName: Guideless type III CRISPR complex from Dissulfurispira thermophila
Components
  • Complex: Guideless type III CRISPR complex from Dissulfurispira thermophila
    • Protein or peptide: CSD domain-containing protein Cmr6
    • Protein or peptide: Type III-B CRISPR-associated protein Cas10/Cmr2
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR type III-B/RAMP module-associated protein Cmr5
    • Protein or peptide: Type III-B CRISPR module-associated protein Cmr3
  • Ligand: ZINC ION

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Supramolecule #1: Guideless type III CRISPR complex from Dissulfurispira thermophila

SupramoleculeName: Guideless type III CRISPR complex from Dissulfurispira thermophila
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Dissulfurispira thermophila (bacteria) / Strain: T55J

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Macromolecule #1: CSD domain-containing protein Cmr6

MacromoleculeName: CSD domain-containing protein Cmr6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria) / Strain: T55J
Molecular weightTheoretical: 42.396605 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSEKGKIKTF KKAKGFGFIK YSGGEIFFHI NDVIASDSDK IKEGIDVEFE IGKGKEGKPA AKKIKVKSLY RQQNIPINDD ISGINYFLP KDTYAAVKPE QIDNFNLLLN KIPYFDGKKF NFYKKDKKRN EILNLARRFN YNASFIKRLS ERHKNSISQL L GSGSITST ...String:
MSEKGKIKTF KKAKGFGFIK YSGGEIFFHI NDVIASDSDK IKEGIDVEFE IGKGKEGKPA AKKIKVKSLY RQQNIPINDD ISGINYFLP KDTYAAVKPE QIDNFNLLLN KIPYFDGKKF NFYKKDKKRN EILNLARRFN YNASFIKRLS ERHKNSISQL L GSGSITST TLSPDWRFII GIGNESVYET SITLHHIYGI PYIPGQAVKG VVRSWIITEV FGQDEKKALK DALFCHIFGS PK ESAIGEH QGSVIFFDAL PITLPQLEVD VMNPHYGDYY QGKEKSNKPV PPADYLNPNP IPFLTVGKDT KFEFTVGMKK LKQ AREVLK NGSSRLISEC EGLTAEKNLH EIAISWLKKA LTEHGIGAKT AVGYGYFEKT

UniProtKB: CSD domain-containing protein

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Macromolecule #2: Type III-B CRISPR-associated protein Cas10/Cmr2

MacromoleculeName: Type III-B CRISPR-associated protein Cas10/Cmr2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria) / Strain: T55J
Molecular weightTheoretical: 70.288859 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGHHHHHHLE VLFQGPMENK FLFLFTITPV QSFINQARKA QDLYAGSFML SHFSKAAANK LKMEFDCEII FPDIANNSIP NRFAAVVNV NENEAQAVGD SLQKAVEAEI KRIGDSVING LKINKPNGFD EQLSSYFTVS YLFVPYNEDD YKQCYSELES L MGAIKSVR ...String:
MGHHHHHHLE VLFQGPMENK FLFLFTITPV QSFINQARKA QDLYAGSFML SHFSKAAANK LKMEFDCEII FPDIANNSIP NRFAAVVNV NENEAQAVGD SLQKAVEAEI KRIGDSVING LKINKPNGFD EQLSSYFTVS YLFVPYNEDD YKQCYSELES L MGAIKSVR AFSQYPDSER GRKCSICGER NVKFYRMAEN EKDIERIKKL KLFSNDVYAV KNSDYRELGP RYLQAGEGLC GV CFTKRGL DRAGIPEYKA KFPSTSKIAL FDAFKQLREK RGDLGTIIDS DNYEPQGIFA LKNNKNLDDF PELSEMEKKN TRE LYEAME DYKISYSPYY AVMLFDGDSM GEWLSGNKIK DEKLKEFHKE LTKKLGEFAN AVRDTIKEPL GVTVYAGGED FLGF FNIKY LLEGMKHLRN KFNELVNLPL KDFYADNTYN MTFSAGAVIA HIKTPLSEVL NWARKVEQEA KDIDDTKDAF AIAVL KHSG EIEKTVFKWR VNDTYTTDLM SKIVTEINND RLSNTFIKKL NQELIKLLDK DGNYRDDNII KAEIKRLLMR SFMKTK DED EDAFKKRKAE TAKELQLHNL LIHSNGVRNF LNFLNITDFI ARQAKGGAA

UniProtKB: Type III-B CRISPR-associated protein Cas10/Cmr2

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Macromolecule #3: Type III-B CRISPR module RAMP protein Cmr4

MacromoleculeName: Type III-B CRISPR module RAMP protein Cmr4 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria) / Strain: T55J
Molecular weightTheoretical: 34.96666 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MFKKARPFFI ICETPLHCGS GNDIGNVDLP IQRERHTDFP KIEASSLKGG IREAFEEADK DIKVGSLTIN ISDKSTISLA FGPEQGSDH AGALGFTDAR ILLFPVKSMK GVFAWVTCPQ VLERFKSDLN LCGVNLGFEM PQANTAPKDC SLFINGNKIV L EEYTFEIA ...String:
MFKKARPFFI ICETPLHCGS GNDIGNVDLP IQRERHTDFP KIEASSLKGG IREAFEEADK DIKVGSLTIN ISDKSTISLA FGPEQGSDH AGALGFTDAR ILLFPVKSMK GVFAWVTCPQ VLERFKSDLN LCGVNLGFEM PQANTAPKDC SLFINGNKIV L EEYTFEIA RDRDESGNCT SLANWLSENL FLANSGIQFW KEKIKKDIVV ISDDEFRDFV TLSTEVITRT KINNETGTVQ SG ALFTEEY LPTDTVLYSL ALTTPVFKEK DEEKGIFKQD SANEEDMVME FFTTGLPEII QLGGNATIGK GIARVKIL

UniProtKB: Type III-B CRISPR module RAMP protein Cmr4

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Macromolecule #4: CRISPR type III-B/RAMP module-associated protein Cmr5

MacromoleculeName: CRISPR type III-B/RAMP module-associated protein Cmr5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria) / Strain: T55J
Molecular weightTheoretical: 15.953378 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MTDNNLTIQK SIERQRAAFA YKCAEAGKSI TKSKEYKAYV KNIPMLIKTN GIGATFAFVK AKSEADVDKS GYAYKLIYEQ TTEWLKQEP KGLIYEKLNN TDMVKALVEL DSDKYRAVTN EVLALFVWLK RFAEGLIEGE K

UniProtKB: CRISPR type III-B/RAMP module-associated protein Cmr5

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Macromolecule #5: Type III-B CRISPR module-associated protein Cmr3

MacromoleculeName: Type III-B CRISPR module-associated protein Cmr3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria) / Strain: T55J
Molecular weightTheoretical: 40.201371 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKRITINALD VLFLRDGKPF TMGSDTWGSG ISLPYPSMIY GVLRSLYFSH NISMLKHAAP IDELNHNDPT RNLKIKGIYL KRASDLLFP VPMDCVVLKN SRDEKLIPLM PVKAQCISNC KTSAVLRPEK GEQIESAEDG WIDKAAMEEY LNGIYENMSY S KLSDFVLS ...String:
MKRITINALD VLFLRDGKPF TMGSDTWGSG ISLPYPSMIY GVLRSLYFSH NISMLKHAAP IDELNHNDPT RNLKIKGIYL KRASDLLFP VPMDCVVLKN SRDEKLIPLM PVKAQCISNC KTSAVLRPEK GEQIESAEDG WIDKAAMEEY LNGIYENMSY S KLSDFVLS EAKIGIARNN KTHIAEDSML YRVGMKRLKD TTIVVDIDGL EIPDAGIIKI GGEGRPASFK AIDIDETSIL QP AINSNKI EKIKLYIATP AIFKKGWLPQ TIDDRDLEGE INGIGLKLIT AAIGRPLYVG GFDIKKGPKP MKRAVPAGSV YYF EIHGQY SNEQIINALH DKAISDREQD RQQGFGIAYV GKWE

UniProtKB: Type III-B CRISPR module-associated protein Cmr3

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.13 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMKClPotassium Chloride
25.0 mMC8H18N2O4SHEPES
50.0 mL/LC3H8O3Glycerol
1.0 mMC9H15O6PTCEP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3251401
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.2) / Software - details: Patch CTF-Correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Software - details: Non-Uniform Refinement / Number images used: 305242
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2) / Software - details: Ab Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2) / Software - details: Non-Uniform Refinement
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1.2) / Software - details: Ab Initio Reconstruction

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Atomic model buiding 1

Initial model
ChainDetails
chain_id: A, residue_range: 1-596, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold (purification tag not included)
chain_id: B, residue_range: 1-360, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold
chain_id: C, residue_range: 1-315, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold
chain_id: D, residue_range: 1-315, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold
chain_id: E, residue_range: 1-315, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold
chain_id: F, residue_range: 1-140, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold
chain_id: G, residue_range: 1-140, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold
chain_id: H, residue_range: 75-376, source_name: AlphaFold, initial_model_type: in silico modelInitial model generated using Alphafold (after trimming N-terminal domain)
SoftwareName: UCSF ChimeraX (ver. 1.6.1)
Details: Fit in Map command was used to dock individual subunits
DetailsInitial local fitting was done using ChimeraX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9arw:
Structure of the guideless DtCmr Type III CRISPR complex

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