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

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Basic information

Entry
Database: PDB / ID: 9arw
TitleStructure of the guideless DtCmr Type III CRISPR complex
Components
  • (Type III-B CRISPR ...) x 2
  • CRISPR type III-B/RAMP module-associated protein Cmr5
  • CSD domain-containing protein Cmr6
  • Type III-B CRISPR-associated protein Cas10/Cmr2
KeywordsIMMUNE SYSTEM / CRISPR / complex / guideless
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBurman, N. / Henriques, W.H. / Pandey, S. / Wiedenheft, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134867-01 United States
Citation
Journal: To Be Published
Title: Structure of a type III CRISPR complex that AMPylates a HEPN toxin
Authors: Pandey, S. / Burman, N. / Henriques, W.H. / Zahl, T. / Wiegand, T. / Nyquist, H. / Wilkinson, R. / Wiedenheft, B.
#1: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
#2: Journal: Nat Methods / Year: 2017
Title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Authors: Ali Punjani / John L Rubinstein / David J Fleet / Marcus A Brubaker /
Abstract: Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a ...Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).
#3: Journal: 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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CSD domain-containing protein Cmr6
A: Type III-B CRISPR-associated protein Cas10/Cmr2
C: Type III-B CRISPR module RAMP protein Cmr4
D: Type III-B CRISPR module RAMP protein Cmr4
E: Type III-B CRISPR module RAMP protein Cmr4
F: CRISPR type III-B/RAMP module-associated protein Cmr5
G: CRISPR type III-B/RAMP module-associated protein Cmr5
B: Type III-B CRISPR module-associated protein Cmr3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,7599
Polymers289,6948
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 4 molecules HAFG

#1: Protein CSD domain-containing protein Cmr6


Mass: 42396.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dissulfurispira thermophila (bacteria) / Strain: T55J / Gene: JZK55_14930 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7G1H339
#2: Protein Type III-B CRISPR-associated protein Cas10/Cmr2


Mass: 70288.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dissulfurispira thermophila (bacteria) / Strain: T55J / Gene: JZK55_14980 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7G1H3Q2
#4: Protein CRISPR type III-B/RAMP module-associated protein Cmr5


Mass: 15953.378 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dissulfurispira thermophila (bacteria) / Strain: T55J / Gene: JZK55_14940 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7G1H353

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Type III-B CRISPR ... , 2 types, 4 molecules CDEB

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


Mass: 34966.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dissulfurispira thermophila (bacteria) / Strain: T55J / Gene: JZK55_14950 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7G1H376
#5: Protein Type III-B CRISPR module-associated protein Cmr3


Mass: 40201.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dissulfurispira thermophila (bacteria) / Strain: T55J / Gene: JZK55_14970 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7G1H1A4

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Guideless type III CRISPR complex from Dissulfurispira thermophila
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Dissulfurispira thermophila (bacteria) / Strain: T55J
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMPotassium ChlorideKCl1
225 mMHEPESC8H18N2O4S1
350 mL/LGlycerolC3H8O31
41 mMTCEPC9H15O6P1
SpecimenConc.: 1.13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.1.2particle selection
4cryoSPARC4.1.2CTF correctionPatch CTF-Correction
7UCSF ChimeraX1.6.1model fittingFit in Map command was used to dock individual subunits
9PHENIX1.20.1_4487:model refinement
10cryoSPARC4.1.2initial Euler assignmentAb Initio Reconstruction
11cryoSPARC4.1.2final Euler assignmentNon-Uniform Refinement
12cryoSPARC4.1.2classificationAb Initio Reconstruction
13cryoSPARC4.1.23D reconstructionNon-Uniform Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3251401
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305242 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: Initial local fitting was done using ChimeraX.
Atomic model building
ID 3D fitting-IDChain-IDChain residue rangeDetailsSource nameType
11A1-596Initial model generated using Alphafold (purification tag not included)AlphaFoldin silico model
21B1-360Initial model generated using AlphafoldAlphaFoldin silico model
31C1-315Initial model generated using AlphafoldAlphaFoldin silico model
41D1-315Initial model generated using AlphafoldAlphaFoldin silico model
51E1-315Initial model generated using AlphafoldAlphaFoldin silico model
61F1-140Initial model generated using AlphafoldAlphaFoldin silico model
71G1-140Initial model generated using AlphafoldAlphaFoldin silico model
81H75-376Initial model generated using Alphafold (after trimming N-terminal domain)AlphaFoldin silico model

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