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- EMDB-38354: Cryo-EM structure of free-state KmAgo -

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Basic information

Entry
Database: EMDB / ID: EMD-38354
TitleCryo-EM structure of free-state KmAgo
Map data
Sample
  • Complex: KmAgo
    • Protein or peptide: KmAgo
  • Ligand: water
KeywordsMesophilic prokaryotic Argonaute / DNA BINDING PROTEIN
Biological speciesKurthia massiliensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsXin T / Hui D / Shaowen W
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2100100 China
CitationJournal: To Be Published
Title: Structural and mechanistic insights into a mesophilic prokaryotic Argonaute
Authors: Xin T / Hui D / Shaowen W
History
DepositionDec 18, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38354.png

Downloads & links

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Map

FileDownload / File: emd_38354.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.856 Å		0.85 Å/pix.
x 256 pix.
= 217.856 Å		0.85 Å/pix.
x 256 pix.
= 217.856 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.502
Minimum - Maximum-2.816977 - 4.027552
Average (Standard dev.)-0.0015643124 (±0.071559966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.856 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38354_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_38354_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 : KmAgo

EntireName: KmAgo
Components
  • Complex: KmAgo
    • Protein or peptide: KmAgo
  • Ligand: water

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Supramolecule #1: KmAgo

SupramoleculeName: KmAgo / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Kurthia massiliensis (bacteria)

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Macromolecule #1: KmAgo

MacromoleculeName: KmAgo / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kurthia massiliensis (bacteria)
Molecular weightTheoretical: 85.485203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEAYITEMVS RERANELEVY VYVFPRKQSD NNYEGVYHIM RAWQRANDLP LAYNQHTIMA FSPVRHMCGY TPMETQKRHI NIDSPFERA LLERLIKNSL IFTAERHLHA KRVGHALRLN QVQQIRQVII YEAIELYVNI IENRISIGFH LTHQFEYVYT L QSMIEQGK ...String:
MEAYITEMVS RERANELEVY VYVFPRKQSD NNYEGVYHIM RAWQRANDLP LAYNQHTIMA FSPVRHMCGY TPMETQKRHI NIDSPFERA LLERLIKNSL IFTAERHLHA KRVGHALRLN QVQQIRQVII YEAIELYVNI IENRISIGFH LTHQFEYVYT L QSMIEQGK TIRPGMRVVH SNGRQHYTYT VENVATYGVT DRCPLLQTSI YQYYVEKGAQ HILRTFTRST RVIHVRTKEQ RL SYAATLL KPLCTFETMQ PQDVLNVSKC IKLSASKRMK CTYRWIQQLR AQYRHLTFAP NPFTIAQNGY KLDQLSTPKV HFH RDYATV VSGMKTGKLY KGGNIKISVL FDEDFYLKHH ITKKDIYQFI AVLQKIAIAQ GVNMTISTST KSITGKFTDD FFHH FTEEV EALQPIFAQT TVLAFITSTH LSNKKTRSYQ LLKQYFGGKW DIASQVITEK TIEAFQKILH KHGLKNFYPN DEQHC LRVI DVLKNESFYY TVMNILLGVY VKSGIQPWIL ANTTHSDCFI GIDVSHENGN SAAGMMNVIG SQGHLIQQAP LNGILA GEK IDDTLLANLL KQMIKAYHTQ FQRFPKHITI HRDGFWREHT ALVEKIMSHY EITYDIVEII KKPNRRMAFF NSVDNTF ST RQGTVYQRGN EAFLCATNPQ QKVGMAQPIK IHQVTKTLPF SHIIEDVYNL SFLHIHAMNK MRLPATIHYA DLSATAYQ R GQVMPRSGNQ TNLPFV

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 23 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 386173
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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