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- PDB-2c8i: Complex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Re... -

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Entry
Database: PDB / ID: 2c8i
TitleComplex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Receptor Decay Accelerating Factor (Cd55) By Cryo Electron Microscopy At 16 A
Components
  • COMPLEMENT DECAY-ACCELERATING FACTOR
  • ECHOVIRUS 11 COAT PROTEIN VP1
  • ECHOVIRUS 11 COAT PROTEIN VP2
  • ECHOVIRUS 11 COAT PROTEIN VP3
  • ECHOVIRUS 11 COAT PROTEIN VP4
KeywordsVIRUS/RECEPTOR / PICORNAVIRUS / DAF / VIRUS-RECEPTOR COMPLEX / ANTIGEN / BLOOD GROUP ANTIGEN / COMPLEMENT PATHWAY / GPI-ANCHOR / IMMUNE RESPONSE / INNATE IMMUNITY / LIPOPROTEIN / PLASMA / SUSHI
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 / 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 ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / 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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / metal ion binding / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / 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 11
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 14 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E
AuthorsPettigrew, D.M. / Williams, D.T. / Kerrigan, D. / Evans, D.J. / Lea, S.M. / Bhella, D.
Citation
Journal: J Biol Chem / Year: 2006
Title: Structural and functional insights into the interaction of echoviruses and decay-accelerating factor.
Authors: David M Pettigrew / David T Williams / David Kerrigan / David J Evans / Susan M Lea / David Bhella /
Abstract: Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo- ...Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo-negative stain transmission electron microscopy and three-dimensional image reconstruction to 16-A resolution, which we interpreted using the atomic structures of EV11 and DAF. DAF binds to a hypervariable region of the capsid close to the 2-fold symmetry axes in an interaction that involves mostly the short consensus repeat 3 domain of DAF and the capsid protein VP2. A bulge in the density for the short consensus repeat 3 domain suggests that a loop at residues 174-180 rearranges to prevent steric collision between closely packed molecules at the 2-fold symmetry axes. Detailed analysis of receptor interactions between a variety of echoviruses and DAF using surface plasmon resonance and comparison of this structure (and our previous work; Bhella, D., Goodfellow, I. G., Roversi, P., Pettigrew, D., Chaudhry, Y., Evans, D. J., and Lea, S. M. (2004) J. Biol. Chem. 279, 8325-8332) with reconstructions published for EV7 bound to DAF support major differences in receptor recognition among these viruses. However, comparison of the electron density for the two virus.receptor complexes (rather than comparisons of the pseudo-atomic models derived from fitting the coordinates into these densities) suggests that the dramatic differences in interaction affinities/specificities may arise from relatively subtle structural differences rather than from large-scale repositioning of the receptor with respect to the virus surface.
#1: Journal: J Biol Chem / Year: 2004
Title: The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
Authors: David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea /
Abstract: Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three- ...Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.
History
DepositionDec 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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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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Assembly

Deposited unit
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)127,9965
Polymers127,9965
Non-polymers00
Water0
1
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 60


Theoretical massNumber of molelcules
Total (without water)7,679,740300
Polymers7,679,740300
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: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 5


  • icosahedral pentamer
  • 640 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)639,97825
Polymers639,97825
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: ECHOVIRUS 11 COAT PROTEIN VP1
B: ECHOVIRUS 11 COAT PROTEIN VP2
C: ECHOVIRUS 11 COAT PROTEIN VP3
D: ECHOVIRUS 11 COAT PROTEIN VP4
E: COMPLEMENT DECAY-ACCELERATING FACTOR
x 6


  • icosahedral 23 hexamer
  • 768 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)767,97430
Polymers767,97430
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: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein ECHOVIRUS 11 COAT PROTEIN VP1 / Coordinate model: Cα atoms only


Mass: 32447.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: P29813
#2: Protein ECHOVIRUS 11 COAT PROTEIN VP2 / Coordinate model: Cα atoms only


Mass: 27996.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: P29813
#3: Protein ECHOVIRUS 11 COAT PROTEIN VP3 / Coordinate model: Cα atoms only


Mass: 25897.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: P29813
#4: Protein ECHOVIRUS 11 COAT PROTEIN VP4 / Coordinate model: Cα atoms only


Mass: 6620.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRUCTURE OF ECHOVIRUS TYPE 11 FITTED INTO CRYO-EM ELECTRON DENSITY FOR ECHOVIRUS TYPE 12. THE EM DENSITY HAS BEEN DEPOSITED IN THE EMDB, WITH ACCESSION CODE 1057
Source: (natural) HUMAN ECHOVIRUS 11 / Strain: GREGORY / References: UniProt: P29813
#5: Protein COMPLEMENT DECAY-ACCELERATING FACTOR / CD55 / Coordinate model: Cα atoms only


Mass: 35034.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08174

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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: ECHOVIRUS TYPE 12 BOUND TO DECAY ACCELERATING FACTOR / Type: VIRUS / Details: CRYO-NEGATIVE STAIN IMAGES. 96 FOCAL PAIRS.
Buffer solutionName: PHOSPHATE BUFFERED SALINE / pH: 7.4 / Details: PHOSPHATE BUFFERED SALINE
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Ammonium Molybdate
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE
Details: STAINED WITH AMMONIUM MOLYBDATE PH 7.2. VITRIFIED IN LIQUID ETHANE (CRYO-NEGATIVE STAIN)

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Electron microscopy imaging

MicroscopyModel: JEOL 1200 / Date: Sep 1, 2004
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000 X / Calibrated magnification: 29100 X / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Cs: 3.4 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 192
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1EM3DR23D reconstruction
2PFT23D reconstruction
CTF correctionDetails: DEFOCUS PAIR IMAGES OF INDIVIDUAL PARTICLES
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: POLAR FOURIER TRANSFORM METHOD / Resolution: 14 Å / Num. of particles: 1501 / Nominal pixel size: 2.18 Å / Actual pixel size: 2.18 Å
Details: THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: OPTIMAL CORRELATION
Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--LOCAL CORRELATION
Atomic model buildingPDB-ID: 1H8T

1h8t

RefinementHighest resolution: 14 Å
Refinement stepCycle: LAST / Highest resolution: 14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 0 0 1091

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