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- EMDB-13136: Subtomogram average of authentic mumps virus nucleocapsid from He... -

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Basic information

Entry
Database: EMDB / ID: EMD-13136
TitleSubtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of short helical pitch
Map dataMinor conformation of authentic mumps virus nucleocapsid from the lysate of HeLa cells after stress treatment by subtomogram averaging
Sample
  • Complex: Authentic Mumps virus nucleocapsid-RNA complex
    • Protein or peptide: Mumps virus nucleocapsid
    • RNA: RNA
Biological speciesMumps virus genotype A
Methodsubtomogram averaging / cryo EM / Resolution: 6.3 Å
AuthorsMahamid J / Zhang X / Pflaesterer T
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067European Union
CitationJournal: To Be Published
Title: A condensate-mediated molecular switch promotes viral replication under stress
Authors: Zhang X / Sridharan S / Zagoriy I / Oegema CE / Ching C / Pflaesterer T / Fung HKH / Poser I / Mueller C / Hyman AA / Savitski MM / Mahamid J
History
DepositionJun 28, 2021-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13136.png

Downloads & links

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Map

FileDownload / File: emd_13136.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMinor conformation of authentic mumps virus nucleocapsid from the lysate of HeLa cells after stress treatment by subtomogram averaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 256 pix.
= 433.613 Å		1.69 Å/pix.
x 256 pix.
= 433.613 Å		1.69 Å/pix.
x 256 pix.
= 433.613 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-0.52652067 - 2.5432017
Average (Standard dev.)0.04158566 (±0.17538643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 433.6128 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Authentic Mumps virus nucleocapsid-RNA complex

EntireName: Authentic Mumps virus nucleocapsid-RNA complex
Components
  • Complex: Authentic Mumps virus nucleocapsid-RNA complex
    • Protein or peptide: Mumps virus nucleocapsid
    • RNA: RNA

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Supramolecule #1: Authentic Mumps virus nucleocapsid-RNA complex

SupramoleculeName: Authentic Mumps virus nucleocapsid-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mumps virus genotype A

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Macromolecule #1: Mumps virus nucleocapsid

MacromoleculeName: Mumps virus nucleocapsid / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mumps virus genotype A / Strain: Enders
SequenceString: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIRL ADRSPEAQIE RCEIDGFEPG TYRLIPNARA NLTANEIAAY ALLADDLPPT INNGTPYVHA DVEGQPCDEI EQFLDRCYSV ...String:
MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIRL ADRSPEAQIE RCEIDGFEPG TYRLIPNARA NLTANEIAAY ALLADDLPPT INNGTPYVHA DVEGQPCDEI EQFLDRCYSV LIQAWVMVCK CMTAYDQPAG SADRRFAKYQ QQGRLEARYM LQPEAQRLIQ TAIRKSLVVR QYLTFELQLA RRQGLLSNRY YAMVGDIGKY IENSGLTAFF LTLKYALGTK WSPLSLAAFT GELTKLRSLM MLYRDIGEQA RYLALLEAPQ IMDFAPGGYP LIFSYAMGVG TVLDAQMRNY TYARPFLNGY YFQIGVETAR RQQGTVDNRV ADDLGLTPEQ RTEVTQLVDR LARGRGAGIP GGPVNPFVPP VQQQQPAAVY ADIPALEESD DDGDEDGGAG FQNGVQVPAV RQGGQTDFRA QPLQDPIQAQ LFMPLYPQVS NIPSNQNHQI NRIGGLENQD LLRYNENGDS QQDARGEHGN TFPNNPNQNA QLQVGDWDE

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2
Source (natural)Organism: Mumps virus genotype A
SequenceString:
UUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 20 / Number images used: 270 / Method: filament tracing / Software: (Name: Dynamo, Warp)
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 3.51 Å
Applied symmetry - Helical parameters - Δ&Phi: -26.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 270
FSC plot (resolution estimation)

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