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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
Specimen sourceYellow fever virus / virus / 黄熱ウイルス
MethodElectron microscopy (Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Nov 26, 2002 / Release: Dec 9, 2003 / Last modification: Feb 24, 2009
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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  • 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)129,6953
Polyers129,6953
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)7,781,683180
Polyers7,781,683180
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)648,47415
Polyers648,47415
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)778,16818
Polyers778,16818
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • 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


Mass: 43231.574 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: Yellow fever immature virus / Aggregation state: PARTICLE
Details: The samples were produced by adding ammonium chloride to the medium in the late infection stage.

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Processing

Image selectionSoftware name: EMFIT
EM single particle entitySymmetry type: ICOSAHEDRAL
Atomic model buildingSoftware name: EMFIT / Ref 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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