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- EMDB-36123: Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36123
TitleCryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex
Map data
Sample
  • Complex: a protein complex
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • Protein or peptide: Uncharacterized protein
    • RNA: RNA (117-MER)
Keywordsa protein complex / VIRAL PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
Uncharacterized protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria) / Haemophilus parainfluenzae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsYin H / Li Z / Yu GM / Li XZ
CitationJournal: To Be Published
Title: Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex
Authors: Yin H / Li Z / Yu GM / Li XZ
History
DepositionMay 5, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36123.png

Downloads & links

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Map

FileDownload / File: emd_36123.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.63
Minimum - Maximum-3.2231185 - 5.2748337
Average (Standard dev.)-0.0014016938 (±0.17069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36123_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36123_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 : a protein complex

EntireName: a protein complex
Components
  • Complex: a protein complex
    • Protein or peptide: CRISPR-associated endonuclease Cas9
    • Protein or peptide: Uncharacterized protein
    • RNA: RNA (117-MER)

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Supramolecule #1: a protein complex

SupramoleculeName: a protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis (bacteria)

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Macromolecule #1: CRISPR-associated endonuclease Cas9

MacromoleculeName: CRISPR-associated endonuclease Cas9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 124.613883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAFKPNSIN YILGLDIGIA SVGWAMVEID EEENPIRLID LGVRVFERAE VPKTGDSLAM ARRLARSVRR LTRRRAHRLL RTRRLLKRE GVLQAANFDE NGLIKSLPNT PWQLRAAALD RKLTPLEWSA VLLHLIKHRG YLSQRKNEGE TADKELGALL K GVAGNAHA ...String:
MAAFKPNSIN YILGLDIGIA SVGWAMVEID EEENPIRLID LGVRVFERAE VPKTGDSLAM ARRLARSVRR LTRRRAHRLL RTRRLLKRE GVLQAANFDE NGLIKSLPNT PWQLRAAALD RKLTPLEWSA VLLHLIKHRG YLSQRKNEGE TADKELGALL K GVAGNAHA LQTGDFRTPA ELALNKFEKE SGHIRNQRSD YSHTFSRKDL QAELILLFEK QKEFGNPHVS GGLKEGIETL LM TQRPALS GDAVQKMLGH CTFEPAEPKA AKNTYTAERF IWLTKLNNLR ILEQGSERPL TDTERATLMD EPYRKSKLTY AQA RKLLGL EDTAFFKGLR YGKDNAEAST LMEMKAYHAI SRALEKEGLK DKKSPLNLSP ELQDEIGTAF SLFKTDEDIT GRLK DRIQP EILEALLKHI SFDKFVQISL KALRRIVPLM EQGKRYDEAC AEIYGDHYGK KNTEEKIYLP PIPADEIRNP VVLRA LSQA RKVINGVVRR YGSPARIHIE TAREVGKSFK DRKEIEKRQE ENRKDREKAA AKFREYFPNF VGEPKSKDIL KLRLYE QQH GKCLYSGKEI NLGRLNEKGY VEIDHALPFS RTWDDSFNNK VLVLGSENQN KGNQTPYEYF NGKDNSREWQ EFKARVE TS RFPRSKKQRI LLQKFDEDGF KERNLNDTRY VNRFLCQFVA DRMRLTGKGK KRVFASNGQI TNLLRGFWGL RKVRAEND R HHALDAVVVA CSTVAMQQKI TRFVRYKEMN AFDGKTIDKE TGEVLHQKTH FPQPWEFFAQ EVMIRVFGKP DGKPEFEEA DTLEKLRTLL AEKLSSRPEA VHEYVTPLFV SRAPNRKMSG QGHMETVKSA KRLDEGVSVL RVPLTQLKLK DLEKMVNRER EPKLYEALK ARLEAHKDDP AKAFAEPFYK YDKAGNRTQQ VKAVRVEQVQ KTGVWVRNHN GIADNATMVR VDVFEKGDKY Y LVPIYSWQ VAKGILPDRA VVQGKDEEDW QLIDDSFNFK FSLHPNDLVE VITKKARMFG YFASCHRGTG NINIRIHDLD HK IGKNGIL EGIGVKTALS FQKYQIDELG KEIRPCRLKK RPPVR

UniProtKB: CRISPR-associated endonuclease Cas9

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Macromolecule #2: Uncharacterized protein

MacromoleculeName: Uncharacterized protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haemophilus parainfluenzae (bacteria)
Molecular weightTheoretical: 9.985316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKITSSNFAT IATSENFAKL SVLPKNHREP IKGLFKSAVE QFSSARDFFK NENYSKELAE KFNKEAVNEA VEKLQKAIDL AEKQGIQF

UniProtKB: Uncharacterized protein

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Macromolecule #3: RNA (117-MER)

MacromoleculeName: RNA (117-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Neisseria meningitidis (bacteria)
Molecular weightTheoretical: 37.367059 KDa
SequenceString:
UAACUUUACG UUGUAGCUCC CUUUCUCGAA AGAGAACCGU UGCUACAAUA AGGCCGUCUG AAAAGAUGUG CCGCAACGCU CUGCCCCUU AAAGCUCCUG CUUUAAGGGG CAUCGUUU

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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: 7.5
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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251996
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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