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- EMDB-38171: Cryo-EM structure of coxsackievirus A16 empty particle in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-38171
TitleCryo-EM structure of coxsackievirus A16 empty particle in complex with Fab h1A6.2 (local refinement)
Map data
Sample
  • Complex: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
    • Complex: The Fab of h1A6.2
      • Protein or peptide: The heavy chain of Fab h1A6.2
      • Protein or peptide: The light chain of Fab h1A6.2
    • Virus: Coxsackievirus A16
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
KeywordsCryo-EM / virus / coxsackievirus A16 / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse) / Coxsackievirus A16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsJiang Y / Huang Y / Zhu R / Zheng Q / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of coxsackievirus A16 empty particle in complex with Fab h1A6.2 (local refinement)
Authors: Jiang Y / Huang Y / Zhu R / Zheng Q / Li S / Xia N
History
DepositionNov 29, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38171.png

Downloads & links

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Map

FileDownload / File: emd_38171.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 200 pix.
= 224. Å		1.12 Å/pix.
x 200 pix.
= 224. Å		1.12 Å/pix.
x 200 pix.
= 224. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.656547 - 4.4636297
Average (Standard dev.)0.015425609 (±0.21820742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 224.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38171_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_38171_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 : Coxsackievirus A16 empty particle in complex with Fab h1A6.2

EntireName: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
Components
  • Complex: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
    • Complex: The Fab of h1A6.2
      • Protein or peptide: The heavy chain of Fab h1A6.2
      • Protein or peptide: The light chain of Fab h1A6.2
    • Virus: Coxsackievirus A16
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein

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Supramolecule #1: Coxsackievirus A16 empty particle in complex with Fab h1A6.2

SupramoleculeName: Coxsackievirus A16 empty particle in complex with Fab h1A6.2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #3: The Fab of h1A6.2

SupramoleculeName: The Fab of h1A6.2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: Coxsackievirus A16

SupramoleculeName: Coxsackievirus A16 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 / NCBI-ID: 31704 / Sci species name: Coxsackievirus A16 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 33.106352 KDa
SequenceString: GDPIADMIDQ TVNNQVNRSL TALQVLPTAA NTEASSHRLG TGVVPALQAA ETGASSNASD KNLIETRCVL NHHSTQETAI GNFFSRAGL VSIITMPTTD TQNTDGYVNW DIDLMGYAQL RRKCELFTYM RFDAEFTFVV AKPNGVLVPQ LLQYMYVPPG A PKPTSRDS ...String:
GDPIADMIDQ TVNNQVNRSL TALQVLPTAA NTEASSHRLG TGVVPALQAA ETGASSNASD KNLIETRCVL NHHSTQETAI GNFFSRAGL VSIITMPTTD TQNTDGYVNW DIDLMGYAQL RRKCELFTYM RFDAEFTFVV AKPNGVLVPQ LLQYMYVPPG A PKPTSRDS FAWQTATNPS VFVKMTDPPA QVSVPFMSPA SAYQWFYDGY PTFGEHLQAN DLDYGQCPNN MMGTFSIRTV GT EKSPHSI TLRVYMRIKH VRAWIPRPLR NQPYLFKTNP NYKGNDIKCT STSRDKITTL

UniProtKB: Genome polyprotein

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 27.557104 KDa
SequenceString: SPSAEACGYS DRVAQLTIGN STITTQEAAN IVIAYGEWPE YCPDTDATAV DKPTRPDVSV NRFFTLDTKS WAKDSKGWYW KFPDVLTEV GVFGQNAQFH YLYRSGFCVH VQCNASKFHQ GALLVAVLPE YVLGTIAGGT GNENSHPPYA TTQPGQVGAV L THPYVLDA ...String:
SPSAEACGYS DRVAQLTIGN STITTQEAAN IVIAYGEWPE YCPDTDATAV DKPTRPDVSV NRFFTLDTKS WAKDSKGWYW KFPDVLTEV GVFGQNAQFH YLYRSGFCVH VQCNASKFHQ GALLVAVLPE YVLGTIAGGT GNENSHPPYA TTQPGQVGAV L THPYVLDA GIPLSQLTVC PHQWINLRTN NCATIIVPYM NTVPFDSALN HCNFGLLVIP VVPLDFNAGA TSEIPITVTI AP MCAEFAG LRQAVKQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 26.654295 KDa
SequenceString: GIPTELKPGT NQFLTTDDGV SAPILPGFHP TPPIHIPGEV HNLLEICRVE TILEVNNLKT NETTPMQRLC FPVSVQSKTG ELCAAFRAD PGRDGPWQST ILGQLCRYYT QWSGSLEVTF MFAGSFMATG KMLIAYTPPG GNVPADRITA MLGTHVIWDF G LQSSVTLV ...String:
GIPTELKPGT NQFLTTDDGV SAPILPGFHP TPPIHIPGEV HNLLEICRVE TILEVNNLKT NETTPMQRLC FPVSVQSKTG ELCAAFRAD PGRDGPWQST ILGQLCRYYT QWSGSLEVTF MFAGSFMATG KMLIAYTPPG GNVPADRITA MLGTHVIWDF G LQSSVTLV VPWISNTHYR AHARAGYFDY YTTGIITIWY QTNYVVPIGA PTTAYIVALA AAQDNFTMKL CKDTEDIEQT AN IQ

UniProtKB: Genome polyprotein

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Macromolecule #4: The heavy chain of Fab h1A6.2

MacromoleculeName: The heavy chain of Fab h1A6.2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.563226 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVQSGAE VKKPGASVKV SCKASGFNIK DFYIHWVRQR PGQGLEWIGW IDPKVGNTMF DPKFQGKARI TVDASISTAY LELSRLRSD DTAVYYCSRG AAAYWGQGTL VTVSS

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Macromolecule #5: The light chain of Fab h1A6.2

MacromoleculeName: The light chain of Fab h1A6.2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.349966 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVVMTQTPLS LPVTLGQPAS ISCKSSQSLL YSDGKTYVNW FQQRPGQSPK RLIYLVSRLD SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCWQGTHL PYTFGQGTKL EIK

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125196
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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