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- EMDB-33182: CryoEM structure of type IV-A Csf-crRNA binary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33182
TitleCryoEM structure of type IV-A Csf-crRNA binary complex
Map data
Sample
  • Complex: Type IV-A Csf-crRNA binary complex
    • Complex: Type IV-A Csf
      • Protein or peptide: Csf1
      • Protein or peptide: Csf3
      • Protein or peptide: Csf2
    • Complex: crRNA
      • RNA: crRNA
  • Ligand: ZINC ION
KeywordsNuclease / STRUCTURAL PROTEIN-RNA COMPLEX
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang JT / Cui N / Huang HD / Jia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Cell / Year: 2023
Title: Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment
Authors: Cui N / Zhang JT / Liu Y / Liu Y / Liu XY / Wang C / Huang H / Jia N
History
DepositionApr 2, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33182.png

Downloads & links

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Map

FileDownload / File: emd_33182.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.0480197 - 0.09793345
Average (Standard dev.)0.000056904657 (±0.0013275564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33182_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33182_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33182_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type IV-A Csf-crRNA binary complex

EntireName: Type IV-A Csf-crRNA binary complex
Components
  • Complex: Type IV-A Csf-crRNA binary complex
    • Complex: Type IV-A Csf
      • Protein or peptide: Csf1
      • Protein or peptide: Csf3
      • Protein or peptide: Csf2
    • Complex: crRNA
      • RNA: crRNA
  • Ligand: ZINC ION

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Supramolecule #1: Type IV-A Csf-crRNA binary complex

SupramoleculeName: Type IV-A Csf-crRNA binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Supramolecule #2: Type IV-A Csf

SupramoleculeName: Type IV-A Csf / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Supramolecule #3: crRNA

SupramoleculeName: crRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4

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Macromolecule #1: Csf1

MacromoleculeName: Csf1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 28.675768 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHHHHH MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLY GLSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR P EVVRKALS ...String:
HHHHHHHHHH MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLY GLSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR P EVVRKALS IADRVNEGQK KWVTPVYFDR KAAAMGHGLI TRAGAEMLTQ EEQEFFQSVT PGERWALSYL MHSKRPEPEV GE CITEKVM TSLNKE

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Macromolecule #2: Csf3

MacromoleculeName: Csf3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 24.421953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVNLKVTIDL SNPMMEPGDL LHLDALLGAL RVSRARAEHG DAINPRDYHY DLPLERYQAP SGDWVFKASA FKLKRQLPNQ MWMQTGRLS IVEAARHRQS GYLQLRAGKP NPAGGPFKTS IYHRPIVQAE LTAFCVGDQQ GIEALLSECR QIGGKRGVGF G QVAGFKVE ...String:
MVNLKVTIDL SNPMMEPGDL LHLDALLGAL RVSRARAEHG DAINPRDYHY DLPLERYQAP SGDWVFKASA FKLKRQLPNQ MWMQTGRLS IVEAARHRQS GYLQLRAGKP NPAGGPFKTS IYHRPIVQAE LTAFCVGDQQ GIEALLSECR QIGGKRGVGF G QVAGFKVE PVAETDCPWS WRALPADADP RLVTSEHARC IAAIRGPYWD RTLHVEALAP TP

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Macromolecule #3: Csf2

MacromoleculeName: Csf2 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 37.322234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQIEVTVRNI TPIFSAAPGS NYITIDGTIN PPPGVSRFPL VRTRMMYVAA DVGDGVIKSV PLQIVPGNTM RSLLRRTMLK HVIEPALVE KGNKLSIGAY ATAYSGNATG NPDGVPSSFD EIATMRAHPF IGLFGGGPRM LEGRLMVDSL YPIHTNAERI L GAGYENEM ...String:
MQIEVTVRNI TPIFSAAPGS NYITIDGTIN PPPGVSRFPL VRTRMMYVAA DVGDGVIKSV PLQIVPGNTM RSLLRRTMLK HVIEPALVE KGNKLSIGAY ATAYSGNATG NPDGVPSSFD EIATMRAHPF IGLFGGGPRM LEGRLMVDSL YPIHTNAERI L GAGYENEM MSGPITQVVW ARRMDPILNL GSSEDVEVIN GGAVAANGWI QDLLANSKAA ASKKKKAAAD EDESDGAAEE NG RGLKAFN AHEVVIPGLK WVWRISLDRP TDAQVGLVLL ALNKMTNERI AGGHSKDYGR FVIDGVSLNG EQVWSQSGIT GGE QYFDAV AEAIDGLSSK EFEQFAQSAK EA

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Macromolecule #4: crRNA

MacromoleculeName: crRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 19.837855 KDa
SequenceString:
GUGAACGGUG GAGCAACACC UGAAGGAAGG CUUGAUGAGC GUGUUCCCCG CAUACGCGGG G

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25016
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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