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- EMDB-39861: Cryo-EM structure of NTR-bound type 7 CRISPR-Cas complex at subst... -

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Basic information

Entry
Database: EMDB / ID: EMD-39861
TitleCryo-EM structure of NTR-bound type 7 CRISPR-Cas complex at substrate-engaged state 2
Map data
Sample
  • Complex: protein structure
    • Protein or peptide: Protein structure
    • Protein or peptide: Protein structure
    • Protein or peptide: Protein structure
    • RNA: RNA (39-MER)
    • RNA: RNA (34-MER)
  • Ligand: ZINC ION
Keywordsprotein structure / ANTIVIRAL PROTEIN
Biological speciesmetagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsZhang H / Deng Z / Li X
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Cryo-EM structure of NTR-bound type 7 CRISPR-Cas complex at substrate-engaged state 2.
Authors: Zhang H / Deng Z / Li X
History
DepositionApr 23, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39861.png

Downloads & links

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Map

FileDownload / File: emd_39861.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.106
Minimum - Maximum-0.86998796 - 1.6526893
Average (Standard dev.)0.0016093662 (±0.040466934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39861_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_39861_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 : protein structure

EntireName: protein structure
Components
  • Complex: protein structure
    • Protein or peptide: Protein structure
    • Protein or peptide: Protein structure
    • Protein or peptide: Protein structure
    • RNA: RNA (39-MER)
    • RNA: RNA (34-MER)
  • Ligand: ZINC ION

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Supramolecule #1: protein structure

SupramoleculeName: protein structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: metagenome (others)

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Macromolecule #1: Protein structure

MacromoleculeName: Protein structure / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 22.255604 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKTMKKIYV TMKTLSPLYT GEVRREDKEA AQKRVNFPVR KTATNKVLIP FKGALRSALE IMLKAKGENV CDTGESRARP CGRCVTCSL FGSMGRAGRA SVDFLISNDT KEQIVRESTH LRIERQTKSA SDTFKGEEVI EGATFTATIT ISNPQEKDLS L IQSALKFI ...String:
MAKTMKKIYV TMKTLSPLYT GEVRREDKEA AQKRVNFPVR KTATNKVLIP FKGALRSALE IMLKAKGENV CDTGESRARP CGRCVTCSL FGSMGRAGRA SVDFLISNDT KEQIVRESTH LRIERQTKSA SDTFKGEEVI EGATFTATIT ISNPQEKDLS L IQSALKFI EENGIGGWLN KGYGRVSFEV KSEDVATDRF LK

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Macromolecule #2: Protein structure

MacromoleculeName: Protein structure / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 27.139533 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEIKGILES ITGFSIPLDN GEYALYPAGR HLRGAIGYIA FNLDLPISSK FLDFDFDDII FRDLLPISKC GKIFYPEKNS NSLKCPSCN EIYGSSVLRN IMARGLSYKE VIEGKKYRLS IIVKDEKYLN EMEAIIRYIL SYGIYLGNKV SKGYGKFKIK E YSIVDILP ...String:
MKEIKGILES ITGFSIPLDN GEYALYPAGR HLRGAIGYIA FNLDLPISSK FLDFDFDDII FRDLLPISKC GKIFYPEKNS NSLKCPSCN EIYGSSVLRN IMARGLSYKE VIEGKKYRLS IIVKDEKYLN EMEAIIRYIL SYGIYLGNKV SKGYGKFKIK E YSIVDILP VKDSEVLLLS DAIIDNGEKD IVFSKKEISS SKFEIIRKRG KAKGDIIRDN NHNGFYIGKY GGLGFGEIIS LK

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Macromolecule #3: Protein structure

MacromoleculeName: Protein structure / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 70.468898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKFIGGASK VTGSAFLLET GNAKILIDCG IEQEKGIEKD NNEIIEKKIN EIGKADICIL THAHLAASGL VPLLVKKRKV NKIISTPAT KELCRLLFND FQRIQEENND IPLYSYDDIE SSFEIWDEID DRNTIELFDT KITFYNNSHI IGSVSVFIET H NGNYLFSG ...String:
MIKFIGGASK VTGSAFLLET GNAKILIDCG IEQEKGIEKD NNEIIEKKIN EIGKADICIL THAHLAASGL VPLLVKKRKV NKIISTPAT KELCRLLFND FQRIQEENND IPLYSYDDIE SSFEIWDEID DRNTIELFDT KITFYNNSHI IGSVSVFIET H NGNYLFSG DIGSKLQQLM DYPPDMPDGN VDYLILESTY GNKSHDSSDR DRLLEIAKTT CENGGKVLIP SFAIGRLQEV LY TFSNYNF NFPVYIDSPM GSKVTNLIKE YNIYLKKKLR RLSITDDLFN NKYIAINTSN QSKELSNSKE PAVIISASGM LEG GRILNH LEQIKNDENS TLIFVGYQAQ NTRGRKILDG EEKVRCRIEK LNSFSAHADQ DELIDYIERL KYTPYKVFLV HGEK EQREI LAKRIISKKI RVELPENYSQ GKEILIEKKV VLNINTDNMC NFASYRLMPF SGFIVEKDDR IEINDKNWFD MIWNE EYNK MRSQIVAEDF STDQNEDSMA LPDMSHDKII ENIEYLFNIK ILSKNRIKEF WEEFCKGQKA AIKYITQVHR KNPNTG RRN WNPPEGDFTD NEIEKLYETA YNTLLSLIKY DKNKVYNILI NFNPKL

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Macromolecule #4: RNA (39-MER)

MacromoleculeName: RNA (39-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 19.142277 KDa
SequenceString:
GGUUAAAACU CUUCUCAUGC UGGAUUCGAA AUUAGGUGCG CUUCGCGUUU AAGUCCCAUA

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Macromolecule #5: RNA (34-MER)

MacromoleculeName: RNA (34-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 19.354707 KDa
SequenceString:
GAACAGAAGA ACACCUAAAC GCGAAGCGCA CCUAAUUUCG AAUCCAGCAU GAGAAGCUAA

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 7 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133899
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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