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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


negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / RNA-protein covalent cross-linking / respiratory burst / : / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / RNA-protein covalent cross-linking / respiratory burst / : / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / complement activation, classical pathway / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / secretory granule membrane / host cell cytoplasmic vesicle membrane / Regulation of Complement cascade / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / positive regulation of T cell cytokine production / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / virus receptor activity / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / Golgi membrane / innate immune response / DNA-templated transcription / lipid binding / host cell nucleus / Neutrophil degranulation / structural molecule activity / virion attachment to host cell / cell surface / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain ...Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Complement decay-accelerating factor / Genome polyprotein
Similarity search - Component
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.
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
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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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Structure viewerMolecule:
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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
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
identity operation1_555x,y,z1
point symmetry operation4
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
identity operation1_555x,y,z1
point symmetry operation5
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 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 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 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 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-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11G40

1g40
PDB Unreleased entry

11G401PDBexperimental model
21COV

1cov

11COV2PDBexperimental model
31EV1

1ev1

11EV13PDBexperimental model
RefinementHighest resolution: 16 Å
Refinement stepCycle: LAST / Highest resolution: 16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 0 0 1013

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