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- PDB-9j9e: Cryo-EM structure of the type VII CRISPR-Cas14 effector complex -

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Basic information

Entry
Database: PDB / ID: 9j9e
TitleCryo-EM structure of the type VII CRISPR-Cas14 effector complex
Components
  • Cas14
  • Cas5
  • Cas7
  • crRNA
  • tgRNA
KeywordsRNA BINDING PROTEIN/RNA / beta-CASP / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSpirochaetota bacterium (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsHiraizumi, M. / Yamashita, K. / Nishimasu, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of type VII CRISPR-Cas14 effector complex
Authors: Hiraizumi, M.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data 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
A: crRNA
B: tgRNA
C: Cas5
D1: Cas7
D2: Cas7
D3: Cas7
D4: Cas7
D5: Cas7
D6: Cas7
D7: Cas7
D8: Cas7
E1: Cas14
E2: Cas14
E3: Cas14
E4: Cas14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)539,16228
Polymers538,31115
Non-polymers85013
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain crRNA


Mass: 19080.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain tgRNA


Mass: 31726.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 3 types, 13 molecules CD1D2D3D4D5D6D7D8E1E2E3E4

#3: Protein Cas5


Mass: 27139.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaetota bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#4: Protein
Cas7


Mass: 22255.604 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaetota bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#5: Protein
Cas14


Mass: 70579.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaetota bacterium (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 13 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / 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: The type VII CRISPR-Cas14 effector complex / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7Cootmodel fitting
9Servalcatmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74619 / Symmetry type: POINT
RefinementResolution: 2.97→2.97 Å / Num. reflection obs: 5430721 / Average fsc work: 0.725
Displacement parametersBiso mean: 81.16 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0097290730.0118
ELECTRON MICROSCOPYs_angle_nonh_deg1.7112395561.8469
ELECTRON MICROSCOPYs_dihedral_angle_1_deg7.219933165.0905
ELECTRON MICROSCOPYs_dihedral_angle_2_deg1.23079214.3811
ELECTRON MICROSCOPYs_dihedral_angle_3_deg10.5167739610
ELECTRON MICROSCOPYs_dihedral_angle_6_deg12.5347146510
ELECTRON MICROSCOPYs_chiral_restr0.127845350.1343
ELECTRON MICROSCOPYs_planes0.0043388410.02
ELECTRON MICROSCOPYs_nbd0.1474318370.2
ELECTRON MICROSCOPYs_nbtor0.1848479480.2
ELECTRON MICROSCOPYs_hbond_nbd0.1098800.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.9-2.919ELECTRON MICROSCOPY1037770.3597
2.919-2.94ELECTRON MICROSCOPY1164810.3834
2.94-2.962ELECTRON MICROSCOPY1136470.4021
2.962-2.984ELECTRON MICROSCOPY1131570.4207
2.984-3.007ELECTRON MICROSCOPY1107610.4446
3.007-3.03ELECTRON MICROSCOPY1104970.4641
3.03-3.053ELECTRON MICROSCOPY1069590.4849
3.053-3.076ELECTRON MICROSCOPY1062130.5044
3.076-3.1ELECTRON MICROSCOPY1053330.5215
3.1-3.125ELECTRON MICROSCOPY1027510.5362
3.125-3.149ELECTRON MICROSCOPY1010250.5517
3.149-3.174ELECTRON MICROSCOPY990370.5705
3.175-3.2ELECTRON MICROSCOPY991270.5985
3.2-3.226ELECTRON MICROSCOPY962850.6315
3.226-3.252ELECTRON MICROSCOPY951250.6577
3.252-3.279ELECTRON MICROSCOPY936210.6788
3.279-3.306ELECTRON MICROSCOPY922150.6975
3.306-3.334ELECTRON MICROSCOPY909010.7151
3.334-3.362ELECTRON MICROSCOPY883890.7285
3.362-3.39ELECTRON MICROSCOPY869470.7375
3.391-3.42ELECTRON MICROSCOPY864930.7388
3.42-3.449ELECTRON MICROSCOPY849250.7421
3.45-3.479ELECTRON MICROSCOPY824970.75
3.48-3.51ELECTRON MICROSCOPY820510.7619
3.51-3.541ELECTRON MICROSCOPY803290.7706
3.542-3.573ELECTRON MICROSCOPY789330.7743
3.573-3.605ELECTRON MICROSCOPY766990.779
3.605-3.638ELECTRON MICROSCOPY759570.7813
3.638-3.672ELECTRON MICROSCOPY753250.7863
3.672-3.706ELECTRON MICROSCOPY731550.797
3.706-3.741ELECTRON MICROSCOPY717970.8134
3.741-3.776ELECTRON MICROSCOPY702970.8295
3.776-3.812ELECTRON MICROSCOPY702690.8419
3.812-3.849ELECTRON MICROSCOPY669430.8486
3.849-3.887ELECTRON MICROSCOPY668610.8528
3.887-3.925ELECTRON MICROSCOPY654970.8552
3.925-3.964ELECTRON MICROSCOPY640950.8559
3.964-4.004ELECTRON MICROSCOPY629050.8566
4.004-4.044ELECTRON MICROSCOPY610450.8594
4.045-4.086ELECTRON MICROSCOPY611490.8654
4.086-4.128ELECTRON MICROSCOPY593830.8704
4.129-4.172ELECTRON MICROSCOPY579450.8743
4.172-4.216ELECTRON MICROSCOPY561610.8782
4.216-4.261ELECTRON MICROSCOPY553630.8821
4.261-4.307ELECTRON MICROSCOPY542730.8872
4.307-4.354ELECTRON MICROSCOPY531730.8942
4.354-4.402ELECTRON MICROSCOPY518850.898
4.402-4.451ELECTRON MICROSCOPY512950.896
4.451-4.501ELECTRON MICROSCOPY498450.8938
4.502-4.553ELECTRON MICROSCOPY486370.8911
4.553-4.606ELECTRON MICROSCOPY472390.8915
4.606-4.659ELECTRON MICROSCOPY465690.8928
4.66-4.715ELECTRON MICROSCOPY457690.895
4.715-4.771ELECTRON MICROSCOPY440670.8965
4.772-4.828ELECTRON MICROSCOPY432730.8946
4.829-4.888ELECTRON MICROSCOPY423330.8909
4.888-4.949ELECTRON MICROSCOPY415930.8861
4.949-5.011ELECTRON MICROSCOPY400150.8793
5.011-5.075ELECTRON MICROSCOPY391890.8724
5.075-5.14ELECTRON MICROSCOPY378610.8675
5.141-5.208ELECTRON MICROSCOPY374550.8652
5.208-5.276ELECTRON MICROSCOPY363730.863
5.277-5.347ELECTRON MICROSCOPY350130.8589
5.348-5.42ELECTRON MICROSCOPY348490.8549
5.421-5.495ELECTRON MICROSCOPY333430.8474
5.495-5.572ELECTRON MICROSCOPY328650.8403
5.572-5.651ELECTRON MICROSCOPY312850.8351
5.651-5.731ELECTRON MICROSCOPY306030.8278
5.733-5.816ELECTRON MICROSCOPY303130.8164
5.816-5.902ELECTRON MICROSCOPY287410.8015
5.902-5.99ELECTRON MICROSCOPY284550.7928
5.991-6.082ELECTRON MICROSCOPY271570.7916
6.083-6.176ELECTRON MICROSCOPY270450.7994
6.177-6.273ELECTRON MICROSCOPY257770.8029
6.276-6.374ELECTRON MICROSCOPY244350.7963
6.375-6.477ELECTRON MICROSCOPY242770.7866
6.478-6.584ELECTRON MICROSCOPY233170.7724
6.585-6.695ELECTRON MICROSCOPY228510.7683
6.696-6.809ELECTRON MICROSCOPY217450.7766
6.811-6.928ELECTRON MICROSCOPY210330.788
6.929-7.05ELECTRON MICROSCOPY207130.7909
7.052-7.178ELECTRON MICROSCOPY196470.7936
7.179-7.309ELECTRON MICROSCOPY188410.7957
7.31-7.444ELECTRON MICROSCOPY182170.8037
7.447-7.588ELECTRON MICROSCOPY177270.8118
7.589-7.735ELECTRON MICROSCOPY171250.8094
7.738-7.886ELECTRON MICROSCOPY161250.8062
7.889-8.047ELECTRON MICROSCOPY158710.8019
8.049-8.213ELECTRON MICROSCOPY152250.7993
8.215-8.386ELECTRON MICROSCOPY145330.7975
8.388-8.566ELECTRON MICROSCOPY137530.8024
8.568-8.752ELECTRON MICROSCOPY130590.8084
8.757-8.951ELECTRON MICROSCOPY129730.8079
8.956-9.157ELECTRON MICROSCOPY120210.8043
9.159-9.37ELECTRON MICROSCOPY117310.8102
9.375-9.598ELECTRON MICROSCOPY109810.8187
9.601-9.835ELECTRON MICROSCOPY107250.8162
9.838-10.084ELECTRON MICROSCOPY101170.8155
10.087-10.345ELECTRON MICROSCOPY93750.8169
10.349-10.617ELECTRON MICROSCOPY91330.8359
10.625-10.912ELECTRON MICROSCOPY85770.8563
10.916-11.219ELECTRON MICROSCOPY82270.8657
11.224-11.539ELECTRON MICROSCOPY75970.8695
11.549-11.889ELECTRON MICROSCOPY73770.8775
11.894-12.254ELECTRON MICROSCOPY69010.8858
12.26-12.643ELECTRON MICROSCOPY63030.8943
12.649-13.057ELECTRON MICROSCOPY60730.9017
13.064-13.492ELECTRON MICROSCOPY56130.904
13.507-13.972ELECTRON MICROSCOPY52750.9059
13.981-14.48ELECTRON MICROSCOPY49810.9051
14.49-15.015ELECTRON MICROSCOPY45330.9089
15.037-15.615ELECTRON MICROSCOPY43030.9117
15.627-16.251ELECTRON MICROSCOPY40170.911
16.265-16.942ELECTRON MICROSCOPY35650.9058
16.957-17.694ELECTRON MICROSCOPY33010.8949
17.711-18.495ELECTRON MICROSCOPY29910.8828
18.535-19.417ELECTRON MICROSCOPY28570.8772
19.44-20.411ELECTRON MICROSCOPY25170.8686
20.464-21.48ELECTRON MICROSCOPY21790.8471
21.543-22.738ELECTRON MICROSCOPY20850.8696
22.775-24.112ELECTRON MICROSCOPY18610.8831
24.157-25.663ELECTRON MICROSCOPY16690.8711
25.824-27.427ELECTRON MICROSCOPY13110.8724
27.492-29.37ELECTRON MICROSCOPY12490.8765
29.531-31.796ELECTRON MICROSCOPY10890.8947
32-34.546ELECTRON MICROSCOPY9070.9069
34.676-37.478ELECTRON MICROSCOPY7290.9172
37.986-41.764ELECTRON MICROSCOPY6250.9119
41.995-46.629ELECTRON MICROSCOPY5710.915
46.952-52.769ELECTRON MICROSCOPY3810.9199
53.238-60.755ELECTRON MICROSCOPY3010.907
61.474-70.428ELECTRON MICROSCOPY2250.9075
72.738-86.938ELECTRON MICROSCOPY1750.9137
89.085-110.496ELECTRON MICROSCOPY1050.9307
115.008-140.856ELECTRON MICROSCOPY490.946
162.646-398.4ELECTRON MICROSCOPY400.8545

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