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Yorodumi- PDB-2c8i: Complex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Re... -
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-Basic information
Entry | Database: PDB / ID: 2c8i | ||||||
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Title | Complex 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 |
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Keywords | VIRUS/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 regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / 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 ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / 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 / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / complement activation, classical pathway / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / DNA replication / RNA helicase activity / membrane raft / induction by virus of host autophagy / Golgi membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / innate immune response / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) HUMAN ECHOVIRUS 11 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 14 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E | ||||||
Authors | Pettigrew, 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 |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 2c8i.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c8i.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 2c8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c8i_validation.pdf.gz | 798.4 KB | Display | wwPDB validaton report |
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Full document | 2c8i_full_validation.pdf.gz | 798 KB | Display | |
Data in XML | 2c8i_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 2c8i_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8i ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8i | HTTPS FTP |
-Related structure data
Related structure data | 1182MC 1183MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ECHOVIRUS TYPE 12 BOUND TO DECAY ACCELERATING FACTOR / Type: VIRUS / Details: CRYO-NEGATIVE STAIN IMAGES. 96 FOCAL PAIRS. |
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Buffer solution | Name: PHOSPHATE BUFFERED SALINE / pH: 7.4 / Details: PHOSPHATE BUFFERED SALINE |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES |
EM staining | Type: NEGATIVE / Material: Ammonium Molybdate |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE Details: STAINED WITH AMMONIUM MOLYBDATE PH 7.2. VITRIFIED IN LIQUID ETHANE (CRYO-NEGATIVE STAIN) |
-Electron microscopy imaging
Microscopy | Model: JEOL 1200 / Date: Sep 1, 2004 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 30000 X / Calibrated magnification: 29100 X / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Cs: 3.4 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 192 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: DEFOCUS PAIR IMAGES OF INDIVIDUAL PARTICLES | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: 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 building | Protocol: OTHER / Space: REAL / Target criteria: OPTIMAL CORRELATION Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--LOCAL CORRELATION | ||||||||||||
Atomic model building | PDB-ID: 1H8T Accession code: 1H8T / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 14 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 14 Å
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