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Yorodumi- PDB-1z7z: Cryo-em structure of human coxsackievirus A21 complexed with five... -
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-Basic information
Entry | Database: PDB / ID: 1z7z | |||||||||
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Title | Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi | |||||||||
Components |
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Keywords | Virus/Receptor / ICAM-1 / Kilifi / CD54 / Human Coxsackievirus A21 / virus-receptor complex / Icosahedral virus | |||||||||
Function / homology | Function and homology information regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / transmembrane signaling receptor activity / integrin binding / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / signaling receptor activity / DNA replication / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / RNA helicase activity / receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / cell adhesion / membrane raft / induction by virus of host autophagy / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human coxsackievirus A21 Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | |||||||||
Authors | Xiao, C. / Bator-Kelly, C.M. / Rieder, E. / Chipman, P.R. / Craig, A. / Kuhn, R.J. / Wimmer, E. / Rossmann, M.G. | |||||||||
Citation | Journal: Structure / Year: 2005 Title: The crystal structure of coxsackievirus A21 and its interaction with ICAM-1. Authors: Chuan Xiao / Carol M Bator-Kelly / Elizabeth Rieder / Paul R Chipman / Alister Craig / Richard J Kuhn / Eckard Wimmer / Michael G Rossmann / Abstract: CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human ...CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 A resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 A resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1(Kilifi). The cryo-EM map was fitted with the crystal structures of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1z7z.cif.gz | 206.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z7z.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 1z7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z7z_validation.pdf.gz | 805 KB | Display | wwPDB validaton report |
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Full document | 1z7z_full_validation.pdf.gz | 824 KB | Display | |
Data in XML | 1z7z_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 1z7z_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/1z7z ftp://data.pdbj.org/pub/pdb/validation_reports/z7/1z7z | HTTPS FTP |
-Related structure data
Related structure data | 1114MC 1z7sC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
-Human coxsackievirus ... , 5 types, 5 molecules 12345
#1: Protein | Mass: 31946.727 Da / Num. of mol.: 1 / Fragment: Viral Protein 1 residues 1073-1286 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: Q7T7N6*PLUS |
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#2: Protein | Mass: 29918.537 Da / Num. of mol.: 1 / Fragment: Viral Protein 2 residues 2010-2272 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: Q7T7N6*PLUS |
#3: Protein | Mass: 25898.895 Da / Num. of mol.: 1 / Fragment: Viral Protein 3 residues 3043-3234 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: Q7T7N6*PLUS |
#4: Protein/peptide | Mass: 1335.565 Da / Num. of mol.: 1 / Fragment: Viral Protein 1 residues 1287-1298 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: P22055*PLUS |
#5: Protein/peptide | Mass: 687.809 Da / Num. of mol.: 1 / Fragment: Viral Protein 3 residues 3035-3239 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569 |
-Protein / Sugars , 2 types, 9 molecules I
#6: Protein | Mass: 49104.473 Da / Num. of mol.: 1 / Fragment: ICAM-1 EXTRACELLULAR DOMAIN 1-5 / Mutation: K29M / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: COS7 / References: UniProt: P05362 |
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#7: Sugar | ChemComp-NAG / |
-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 |
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Details of virus | Host category: MAMMALIAN / Type: VIRION | ||||||||||||||||||||||||||||||||||||||||
Natural host | Organism: Homo sapiens / Strain: Hela | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | Name: TRIS / pH: 7.2 / Details: TRIS | ||||||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: HOLEY CARBON | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: REICHERT-JUNG PLUNGER / Cryogen name: ETHANE / Details: PLUNGED INTO ETHANE AT LIQUID NITROGEN TEMPERATURE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Mar 15, 2001 Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE. |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 26 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 33 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: REVERSED CTF WITH WEINER FACTOR FOR EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: POLAR FOURIER TRANSFORM METHOD AND FOURIER-BESSEL RECONSTRUCTION Resolution: 8 Å / Num. of particles: 4704 / Nominal pixel size: 2.98 Å / Actual pixel size: 2.85 Å Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF THE VIRUS CAPSID. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF ...Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF THE VIRUS CAPSID. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 104 ANGSTROMS AND EXTERNAL RADIUS 177 ANGSTROMS. Details: A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4*LN(0.1*RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCUPANCY OF 1.0 WAS SET FOR ALL ATOMS OF ...Details: A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4*LN(0.1*RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCUPANCY OF 1.0 WAS SET FOR ALL ATOMS OF THE VIRAL CAPSID. OCCUPANCY OF 0.80, 0.56, 0.24, 0.16, AND 0.08 WAS SET FOR ATOMS OF ICAM-1 DOMAIN 1, 2, 3, 4, AND 5, RESPECTIVELY, BASED ON THE FITTING RESULTS. SEE DETAILS IN THE CITATION. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: BEST SUMF VALUE FIT USING THE PROGRAM EMFIT Details: REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
Atomic model building |
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Refinement | Highest resolution: 8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8 Å
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