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- PDB-1m11: structural model of human decay-accelerating factor bound to echo... -

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Entry
Database: PDB / ID: 1m11
Titlestructural model of human decay-accelerating factor bound to echovirus 7 from cryo-electron microscopy
Descriptordecay-accelerating factor/coat protein VP1/coat protein VP2/coat protein VP3
KeywordsVirus/Receptor / decay-accelerating factor / SCR / Icosahedral virus / Virus-Receptor COMPLEX
Specimen sourceHomo sapiens / human
Human echovirus 7 / virus
MethodElectron microscopy (16 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsHe, Y. / Lin, F. / Chipman, P.R. / Bator, C.M. / Baker, T.S. / Shoham, M. / Kuhn, R.J. / Medof, M.E. / Rossmann, M.G.
CitationProc. Natl. Acad. Sci. U.S.A., 2002, 99, 10325-10329

Proc. Natl. Acad. Sci. U.S.A., 2002, 99, 10325-10329 StrPapers
Structure of decay-accelerating factor bound to echovirus 7: a virus-receptor complex.
Yongning He / Feng Lin / Paul R Chipman / Carol M Bator / Timothy S Baker / Menachem Shoham / Richard J Kuhn / M Edward Medof / Michael G Rossmann

DateDeposition: Jun 17, 2002 / Release: Aug 28, 2002 / Last modification: Feb 24, 2009

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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
R: decay-accelerating factor
1: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3


Theoretical massNumber of molelcules
Total (without water)113,4084
Polyers113,4084
Non-polymers00
Water0
#1
R: decay-accelerating factor
1: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
x 60


Theoretical massNumber of molelcules
Total (without water)6,804,454240
Polyers6,804,454240
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
R: decay-accelerating factor
1: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
x 5


  • icosahedral pentamer
  • 567 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)567,03820
Polyers567,03820
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
R: decay-accelerating factor
1: COAT PROTEIN VP1
2: COAT PROTEIN VP2
3: COAT PROTEIN VP3
x 6


  • icosahedral 23 hexamer
  • 680 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)680,44524
Polyers680,44524
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)decay-accelerating factor


Mass: 27017.459 Da / Num. of mol.: 1 / Fragment: four SCR domains 1 to 4 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P08174

Cellular component

Molecular function

Biological process

  • CD4-positive, alpha-beta T cell cytokine production (GO: 0035743)
  • complement activation, classical pathway (GO: 0006958)
  • ER to Golgi vesicle-mediated transport (GO: 0006888)
  • innate immune response (GO: 0045087)
  • negative regulation of complement activation (GO: 0045916)
  • positive regulation of CD4-positive, alpha-beta T cell activation (GO: 2000516)
  • positive regulation of CD4-positive, alpha-beta T cell proliferation (GO: 2000563)
  • positive regulation of cytosolic calcium ion concentration (GO: 0007204)
  • regulation of complement activation (GO: 0030449)
  • regulation of lipopolysaccharide-mediated signaling pathway (GO: 0031664)
  • respiratory burst (GO: 0045730)
#2: Polypeptide(L)COAT PROTEIN VP1


Mass: 31682.660 Da / Num. of mol.: 1 / Source: (gene. exp.) Human echovirus 7 / virus / References: UniProt: Q914E0

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)COAT PROTEIN VP2


Mass: 28443.307 Da / Num. of mol.: 1 / Source: (gene. exp.) Human echovirus 7 / virus / References: UniProt: Q914E0

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)COAT PROTEIN VP3


Mass: 26264.133 Da / Num. of mol.: 1 / Source: (gene. exp.) Human echovirus 7 / virus / References: UniProt: Q914E0

Cellular component

Molecular function

Biological process

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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: human decay-accelerating factor, HUMAN ECHOVIRUS 7 COAT PROTEINS
Aggregation state: PARTICLE
Details: This structure is modeled based on cryo-EM density at 16A resolution.
Buffer solutionName: tris buffer pH7.5
Sample preparationpH: 7.5 / Sample conc.: 8 mg/ml
VitrificationDetails: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER
Crystal grow
*PLUS
Temp unit: K / Method: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Sep 10, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1660 e/A2
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 4200 nm / Nominal defocus min: 1800 nm
Specimen holderTemperature: 120 K

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Processing

Image selectionSoftware name: EMFIT
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: PFT / Resolution: 16 A / Nominal pixel size: 3.11 A/pix / CTF correction method: CTF correction of each micrograph
Details: The echovirus 7 structure is unknown, the model used here is from coxsackievirus B3 (1COV) and echovirus 1 (1EV1).The DAF receptor model is from 1g40. Only CA coordinates are presented in the entry.
Atomic model buildingSoftware name: EMFIT / Ref space: REAL
Atomic model buildingPDB-ID: 1g40, 1cov, 1ev1
Least-squares processHighest resolution: 16 A
Refine hist #LASTHighest resolution: 16 A
Number of atoms included #LASTProtein: 1013 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1013

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