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- PDB-1na4: The structure of immature Yellow Fever virus particle -

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Basic information

Entry
Database: PDB / ID: 1na4
TitleThe structure of immature Yellow Fever virus particle
Descriptormajor envelope protein E
KeywordsVIRUS / flavivirus / flaviviridae / yellow fever immature virus / prM particle / Icosahedral virus / Virus
Specimen sourceYellow fever virus / virus / 黄熱ウイルス
MethodElectron microscopy (Particle / Single particle)
AuthorsZhang, Y. / Corver, J. / Chipman, P.R. / Lenches, E. / Zhang, W. / Pletnev, S.V. / Sedlak, D. / Baker, T.S. / Strauss, J.H. / Kuhn, R.J. / Rossmann, M.G.
CitationEMBO J., 2003, 22, 2604-2613

EMBO J., 2003, 22, 2604-2613 StrPapers
Structures of immature flavivirus particles.
Ying Zhang / Jeroen Corver / Paul R Chipman / Wei Zhang / Sergei V Pletnev / Dagmar Sedlak / Timothy S Baker / James H Strauss / Richard J Kuhn / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 26, 2002 / Release: Dec 9, 2003
RevisionDateData content typeGroupProviderType
1.0Dec 9, 2003Structure modelrepositoryInitial release
1.1Apr 28, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE AUTHORS PROVIDED COORDINATES FOR ALPHA CARBONS ONLY. THE SEQRES RECORDS ARE FROM TICK-BORN ENCEPHALITIS VIRUS BECAUSE THE FITTING MODEL OF MAJOR ENVELOPE PROTEIN E (1SVB) WAS USED IN THIS STUDY.

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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Assembly

Deposited unit
A: major envelope protein E
B: major envelope protein E
C: major envelope protein E


Theoretical massNumber of molelcules
Total (without water)129,6933
Polyers129,6933
Non-polymers00
Water0
#1
A: major envelope protein E
B: major envelope protein E
C: major envelope protein E
x 60


Theoretical massNumber of molelcules
Total (without water)7,781,606180
Polyers7,781,606180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: major envelope protein E
B: major envelope protein E
C: major envelope protein E
x 5


  • icosahedral pentamer
  • 648 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)648,46715
Polyers648,46715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: major envelope protein E
B: major envelope protein E
C: major envelope protein E
x 6


  • icosahedral 23 hexamer
  • 778 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)778,16118
Polyers778,16118
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Polypeptide(L)major envelope protein E / Coordinate model: Cα atoms only


Mass: 43231.145 Da / Num. of mol.: 3
Source: (natural) Yellow fever virus / virus / 黄熱ウイルス
References: UniProt: P14336

Cellular component

Molecular function

Biological process

  • clathrin-dependent endocytosis of virus by host cell (GO: 0075512)
  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • induction by virus of host autophagy (GO: 0039520)
  • regulation of transcription, DNA-templated (GO: 0006355)
  • suppression by virus of host type I interferon-mediated signaling pathway (GO: 0039502)
  • transcription, DNA-templated (GO: 0006351)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Yellow fever immature virus / Type: VIRUS
Details: The samples were produced by adding ammonium chloride to the medium in the late infection stage.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T
Electron gunElectron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1EMFitMODEL FITTING
2CustomRECONSTRUCTIONcommon-line method
SymmetryPoint symmetry: I
3D reconstructionSymmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model buildingPDB-ID: 1SVB
Number of atoms included #LASTProtein: 1185 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1185

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