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- EMDB-9635: The structure of Enterovirus D68 A-particle triggered by an unkno... -

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Basic information

Entry
Database: EMDB / ID: 9635
TitleThe structure of Enterovirus D68 A-particle triggered by an unknown stimulus
Map data
SampleEnterovirus D68Enterovirus 68:
virus / (nucleic-acidNucleic acid) x 3
SourceEnterovirus D68
Methodsingle particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsZheng QB / Zhu R / Xu LF / He MZ / Yan XD / Cheng T / Li SW
CitationJournal: Nat Microbiol / Year: 2019
Title: Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization.
Authors: Qingbing Zheng / Rui Zhu / Longfa Xu / Maozhou He / Xiaodong Yan / Dongxiao Liu / Zhichao Yin / Yangtao Wu / Yongchao Li / Lisheng Yang / Wangheng Hou / Shuxuan Li / Zizhen Li / Zhenqin Chen / Zhihai Li / Hai Yu / Ying Gu / Jun Zhang / Timothy S Baker / Z Hong Zhou / Barney S Graham / Tong Cheng / Shaowei Li / Ningshao Xia
DateDeposition: Aug 27, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 7, 2018 / Last update: Dec 26, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9635.map.gz (map file in CCP4 format, 364501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
450 pix
1.13 Å/pix.
= 507.6 Å
450 pix
1.13 Å/pix.
= 507.6 Å
450 pix
1.13 Å/pix.
= 507.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density
Contour Level:0.048 (by author), 0.048 (movie #1):
Minimum - Maximum-0.10020681 - 0.13266715
Average (Standard dev.)0.001057365 (0.01054751)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions450450450
Origin0.00.00.0
Limit449.0449.0449.0
Spacing450450450
CellA=B=C: 507.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z507.600507.600507.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.1000.1330.001

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Supplemental data

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Sample components

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Entire Enterovirus D68

EntireName: Enterovirus D68 / Number of components: 4

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Component #1: virus, Enterovirus D68

VirusName: Enterovirus D68Enterovirus 68 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Enterovirus D68

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Component #2: nucleic-acid, VP1

Nucleic-acidName: VP1 / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSAAQADKNF FKWTINTRSF VQLRRKLELF TYLRFDAEIT ILTTVAVNGS GNNTYVGLPD LTLQAMFVPT GALTPEKQDS FHWQSGSNAS VFFKISDPPA RITIPFMCIN SAYSVFYDGF AGFEKNGLYG INPADTIGNL CVRIVNEHQP VGFTVTVRVY MKPKHIKAWA PRPPRTLPYM SIANANYKGK ERAPNALNAI IGNRDSVKTM PHNIV
SourceSpecies: Enterovirus D68

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Component #3: nucleic-acid, VP2

Nucleic-acidName: VP2 / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNIG MFGQNVQHHY LYRSGFLIHV QCNATKFHQG ALLVVAIPEH QRGAHNTNTS PGFDDIMKGE EGGTFNHPYV LDDGTSLACA TIFPHQWINL RTNNSATIVL PWMNAAPMDF PLRHNQWTLA IIPVVPLGTR TTSSMVPITV SIAPMCCEFN GLRHAITQ
SourceSpecies: Enterovirus D68

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Component #4: nucleic-acid, VP3

Nucleic-acidName: VP3 / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQL DGPLRNTLVG NISRYYTHWS GSLEMTFMFC GSFMATGKLI LCYTPPGGSC PTTRETAMLG THIVWDFGLQ SSVTLIIPWI SGSHYRMFNN DAKSTNANVG YVTCFMQTNL IVPSESSDTC SLIGFIAAKD DFSLRLMRDS PDIGQLDHLH AAEAAYQ
SourceSpecies: Enterovirus D68

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 2491
3D reconstructionSoftware: RELION / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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