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- EMDB-49920: Structure of Hailong HalA in complex with oligodeoxyadenylate -

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Basic information

Entry
Database: EMDB / ID: EMD-49920
TitleStructure of Hailong HalA in complex with oligodeoxyadenylate
Map dataunsharpened map
Sample
  • Complex: HalA in complex with ODA
    • Protein or peptide: HalA
KeywordsHailong / ion channel / oligodeoxyadenylate / anti-phage defense / ANTIVIRAL PROTEIN
Biological speciesRhodobacteraceae bacterium QY30 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsTan JMJ / Melamed S / Cofsky JC / Syangtan D / Hobbs SJ / Del Marmol J / Jost M / Kruse AC / Sorek R / Kranzusch PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250 United States
CitationJournal: To Be Published
Title: Structure of Hailong HalA in complex with oligodeoxyadenylate
Authors: Tan JMJ / Melamed S / Cofsky JC / Syangtan D / Hobbs SJ / Del Marmol J / Jost M / Kruse AC / Sorek R / Kranzusch PJ
History
DepositionMar 26, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49920.png

Downloads & links

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Map

FileDownload / File: emd_49920.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 384 pix.
= 282.624 Å		0.74 Å/pix.
x 384 pix.
= 282.624 Å		0.74 Å/pix.
x 384 pix.
= 282.624 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0386
Minimum - Maximum-0.07286679 - 0.25197694
Average (Standard dev.)0.0006762307 (±0.0053372714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 282.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49920_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_49920_msk_2.map
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Additional map: density-modified map

Fileemd_49920_additional_1.map
Annotationdensity-modified map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map A

Fileemd_49920_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_49920_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Sample components

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Entire : HalA in complex with ODA

EntireName: HalA in complex with ODA
Components
  • Complex: HalA in complex with ODA
    • Protein or peptide: HalA

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Supramolecule #1: HalA in complex with ODA

SupramoleculeName: HalA in complex with ODA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhodobacteraceae bacterium QY30 (bacteria)

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Macromolecule #1: HalA

MacromoleculeName: HalA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacteraceae bacterium QY30 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH GSLDTNAVKE PEPALPSAAS RGRRTKNWWE PMFDANAPAS FSVSDWNFSN NRGPRCTLFL AEKMPDATTL VVKDIDFQDC DFQGTFERKI VFKDCKFTRC DFGLSTFSRT KFSGCSFYAS SFTQCTLENC EFRNCKYEKI FYSGNETQIP RTLIAEPYQF ...String:
MGSSHHHHHH GSLDTNAVKE PEPALPSAAS RGRRTKNWWE PMFDANAPAS FSVSDWNFSN NRGPRCTLFL AEKMPDATTL VVKDIDFQDC DFQGTFERKI VFKDCKFTRC DFGLSTFSRT KFSGCSFYAS SFTQCTLENC EFRNCKYEKI FYSGNETQIP RTLIAEPYQF LFGACATVDS VPQGKSRFEQ RARFEETRST IARALLANLH SEGSEDTYYA AVKASTLSEN RARIARALIK INSSASKGKS IISRAVSFLT GFASAISAVV GMLILLVMGS LNGWGSSISR AMLVGVVAIS CVAYRYHYRF NLPPEDAMVK ATEIFFLFGY TNYAKMGQED FHLVFSNALL GLFWYAIAIP TISNRLTRAR G

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: 30 s glow, 10 s hold. easiGlow (Pelco). Negative.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 10951 / Average electron dose: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1247992
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 231898
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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