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

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Basic information

Entry
Database: PDB / ID: 1m11
Titlestructural model of human decay-accelerating factor bound to echovirus 7 from cryo-electron microscopy
Components
  • COAT PROTEIN VP1
  • COAT PROTEIN VP2
  • COAT PROTEIN VP3
  • decay-accelerating factor
KeywordsVirus/Receptor / decay-accelerating factor / SCR / Icosahedral virus / Virus-Receptor COMPLEX
Function / homology
Function and homology information


Regulation of Complement cascade / COPI-mediated anterograde transport / Neutrophil degranulation / Class B/2 (Secretin family receptors) / positive regulation of CD4-positive, alpha-beta T cell activation / CD4-positive, alpha-beta T cell cytokine production / negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell proliferation ...Regulation of Complement cascade / COPI-mediated anterograde transport / Neutrophil degranulation / Class B/2 (Secretin family receptors) / positive regulation of CD4-positive, alpha-beta T cell activation / CD4-positive, alpha-beta T cell cytokine production / negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of complement-dependent cytotoxicity / ficolin-1-rich granule membrane / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / transport vesicle / anchored component of membrane / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / complement activation, classical pathway / regulation of complement activation / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / virus receptor activity / positive regulation of cytosolic calcium ion concentration / induction by virus of host autophagy / RNA-directed RNA polymerase / endoplasmic reticulum to Golgi vesicle-mediated transport / ion channel activity / suppression by virus of host gene expression / protein complex oligomerization / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / lipid binding / transcription, DNA-templated / virion attachment to host cell / membrane raft / Golgi membrane / innate immune response / structural molecule activity / neutrophil degranulation / cell surface / RNA binding / extracellular exosome / membrane / extracellular region / ATP binding / plasma membrane
Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Sushi repeat (SCR repeat) / RNA-directed RNA polymerase, C-terminal domain / picornavirus capsid protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Sushi/SCR/CCP domain / Peptidase C3, picornavirus core protein 2A / Sushi/SCR/CCP superfamily ...Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Sushi repeat (SCR repeat) / RNA-directed RNA polymerase, C-terminal domain / picornavirus capsid protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Sushi/SCR/CCP domain / Peptidase C3, picornavirus core protein 2A / Sushi/SCR/CCP superfamily / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Helicase, superfamily 3, single-stranded RNA virus / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Picornavirus coat protein VP4 superfamily / RNA dependent RNA polymerase / Picornavirus capsid / Picornavirus 2B protein / RNA helicase / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Sushi/CCP/SCR domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / Picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain
Complement decay-accelerating factor / Genome polyprotein
Biological speciesHomo sapiens (human)
Human echovirus 7
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å
AuthorsHe, Y. / Lin, F. / Chipman, P.R. / Bator, C.M. / Baker, T.S. / Shoham, M. / Kuhn, R.J. / Medof, M.E. / Rossmann, M.G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2002
Title: Structure of decay-accelerating factor bound to echovirus 7: a virus-receptor complex.
Authors: Yongning He / Feng Lin / Paul R Chipman / Carol M Bator / Timothy S Baker / Menachem Shoham / Richard J Kuhn / M Edward Medof / Michael G Rossmann /
Abstract: Echoviruses are enteroviruses that belong to Picornaviridae. Many echoviruses use decay-accelerating factor (DAF) as their cellular receptor. DAF is a glycosylphosphatidyl inositol-anchored ...Echoviruses are enteroviruses that belong to Picornaviridae. Many echoviruses use decay-accelerating factor (DAF) as their cellular receptor. DAF is a glycosylphosphatidyl inositol-anchored complement regulatory protein found on most cell surfaces. It functions to protect cells from complement attack. The cryo-electron microscopy reconstructions of echovirus 7 complexed with DAF show that the DAF-binding regions are located close to the icosahedral twofold axes, in contrast to other enterovirus complexes where the viral canyon is the receptor binding site. This novel receptor binding position suggests that DAF is important for the attachment of viral particles to host cells, but probably not for initiating viral uncoating, as is the case with canyon-binding receptors. Thus, a different cell entry mechanism must be used for enteroviruses that bind DAF.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name

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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)113,4074
Polymers113,4074
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)6,804,412240
Polymers6,804,412240
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)567,03420
Polymers567,03420
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)680,44124
Polymers680,44124
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
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein/peptide decay-accelerating factor / / Coordinate model: Cα atoms only


Mass: 27017.299 Da / Num. of mol.: 1 / Fragment: four SCR domains 1 to 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P08174
#2: Protein/peptide COAT PROTEIN VP1 / Coordinate model: Cα atoms only


Mass: 31682.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human echovirus 7 / Genus: Enterovirus / Species: Human enterovirus B / Description: RHABDOMYOSARCOMA CELL (RD); / Cell line (production host): RD / Production host: Homo sapiens (human) / Tissue (production host): muscle / References: UniProt: Q914E0
#3: Protein/peptide COAT PROTEIN VP2 / Coordinate model: Cα atoms only


Mass: 28443.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human echovirus 7 / Genus: Enterovirus / Species: Human enterovirus B / Description: RHABDOMYOSARCOMA CELL (RD); / Cell line (production host): RD / Production host: Homo sapiens (human) / Tissue (production host): muscle / References: UniProt: Q914E0
#4: Protein/peptide COAT PROTEIN VP3 / Coordinate model: Cα atoms only


Mass: 26264.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human echovirus 7 / Genus: Enterovirus / Species: Human enterovirus B / Description: RHABDOMYOSARCOMA CELL (RD) / Cell line (production host): RD / Production host: Homo sapiens (human) / Tissue (production host): muscle / References: UniProt: Q914E0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human decay-accelerating factor, HUMAN ECHOVIRUS 7 COAT PROTEINS
Type: VIRUS
Details: This structure is modeled based on cryo-EM density at 16A resolution.
Buffer solutionName: tris buffer pH7.5 / pH: 7.5 / Details: tris buffer pH7.5
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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
Method: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Sep 10, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Nominal defocus max: 4200 nm / Nominal defocus min: 1800 nm
Specimen holderTemperature: 120 K
Image recordingElectron dose: 16.6 e/Å2

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2PFT3D reconstruction
CTF correctionDetails: CTF correction of each micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PFT / Resolution: 16 Å / Nominal pixel size: 3.11 Å
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.
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID3D fitting-ID
11G40

1g40
PDB Unreleased entry

1
21COV1
31EV11
RefinementHighest resolution: 16 Å
Refinement stepCycle: LAST / Highest resolution: 16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 0 0 1013

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