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- PDB-1z7z: Cryo-em structure of human coxsackievirus A21 complexed with five... -

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Entry
Database: PDB / ID: 1z7z
TitleCryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi
Components
  • (human coxsackievirus ...) x 5
  • Intercellular adhesion molecule-1
KeywordsVirus/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 ...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 / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / cellular response to leukemia inhibitory factor / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cellular response to glucose stimulus / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / nucleoside-triphosphate phosphatase / transmembrane signaling receptor activity / integrin binding / protein complex oligomerization / virus receptor activity / signaling receptor activity / monoatomic ion channel activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / RNA helicase activity / DNA replication / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / induction by virus of host autophagy / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / cell surface / proteolysis / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like ...: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / : / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / Immunoglobulin domain / 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 / Immunoglobulin subtype / Immunoglobulin / 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. / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Intercellular adhesion molecule 1 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus A21
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsXiao, C. / Bator-Kelly, C.M. / Rieder, E. / Chipman, P.R. / Craig, A. / Kuhn, R.J. / Wimmer, E. / Rossmann, M.G.
CitationJournal: 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
DepositionMar 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Dec 18, 2019Group: Derived calculations / Other / Category: atom_sites / cell / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,66214
Polymers138,8926
Non-polymers1,7708
Water0
1
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,439,700840
Polymers8,333,520360
Non-polymers106,180480
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules
x 5


  • icosahedral pentamer
  • 703 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)703,30870
Polymers694,46030
Non-polymers8,84840
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 844 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)843,97084
Polymers833,35236
Non-polymers10,61848
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

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Human coxsackievirus ... , 5 types, 5 molecules 12345

#1: Protein human coxsackievirus A21 / Enterovirus C


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
#2: Protein human coxsackievirus A21 / Enterovirus C


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 human coxsackievirus A21 / Enterovirus C


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 human coxsackievirus A21 / Enterovirus C


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 human coxsackievirus A21 / Enterovirus C


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

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Protein / Sugars , 2 types, 9 molecules I

#6: Protein Intercellular adhesion molecule-1 / / ICAM-1 / Major group rhinovirus receptor / CD54


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
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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

Component
IDNameTypeDetailsParent-ID
1COXSACKIEVIRUS A21/ICAM- 1KILIFI COMPLEXVIRUSTHIS STRUCTURE IS MODELED BASED ON CRYO-EM DENSITY AT 8A RESOLUTION.0
2HUMAN COXSACKIEVIRUS A21 VP1 1073-1286Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
3human coxsackievirus A21 VP2 2010-2272Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
4human coxsackievirus A21 VP3 3043-3234Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
5human coxsackievirus A21 VP1 1287-1298Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
6human coxsackievirus A21 VP3 3035-3239Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
7ICAM-1KILIFIApply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
Details of virusHost category: MAMMALIAN / Type: VIRION
Natural hostOrganism: Homo sapiens / Strain: Hela
Buffer solutionName: TRIS / pH: 7.2 / Details: TRIS
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: REICHERT-JUNG PLUNGER / Cryogen name: ETHANE / Details: PLUNGED INTO ETHANE AT LIQUID NITROGEN TEMPERATURE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Mar 15, 2001
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 26 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 33
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2EM3DR3D reconstruction
3PFT3D reconstruction
CTF correctionDetails: REVERSED CTF WITH WEINER FACTOR FOR EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: 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 buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: BEST SUMF VALUE FIT USING THE PROGRAM EMFIT
Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-ID
11IAM

1iam

1
21Z7S

1z7s

1
RefinementHighest resolution: 8 Å
Refinement stepCycle: LAST / Highest resolution: 8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 112 0 8824

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