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- PDB-1z7s: The crystal structure of coxsackievirus A21 -

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Basic information

Entry
Database: PDB / ID: 1z7s
TitleThe crystal structure of coxsackievirus A21
Components(Human COXSACKIEVIRUS ...) x 4
KeywordsVIRUS / PICORNAVIRUS / Coxsackievirus / A21 / Capsid Protein / Viral Protein / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Few Secondary Structures / Irregular / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / MYRISTIC ACID / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus A21
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Remark 600 HETEROGEN THE N-TERMINAL OF VP4 (CHAIN 4) IS MYRISTYLATED WHICH MEANS THE MYR IS COVALENTLY LINKED ... HETEROGEN THE N-TERMINAL OF VP4 (CHAIN 4) IS MYRISTYLATED WHICH MEANS THE MYR IS COVALENTLY LINKED TO THE GLY OF VP4. THEREFORE, THE O2 ATOM ON MYR IS EXPECTED TO BE MISSING AFTER MYRISTYLATED.
Remark 999SEQUENCE THE COMPLETE GENOME SEQUENCE FOR HUMAN COXSACKIEVIRUS A21 IS AVAILABLE AT GENBANK WITH ...SEQUENCE THE COMPLETE GENOME SEQUENCE FOR HUMAN COXSACKIEVIRUS A21 IS AVAILABLE AT GENBANK WITH ACCESSION CODE AF546702 (GI:3304568). THE INDEX OF THIS VIRUS IS 00.052.0.01.005.01.021 WHICH IS AVAILABLE AT ICTVDB: HTTP://WWW.NCBI.NLM.NIH.GOV/ICTVDB/ICTV/INDEX.HTM.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Human COXSACKIEVIRUS A21
2: Human COXSACKIEVIRUS A21
3: Human coxsackievirus A21
4: Human coxsackievirus A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9228
Polymers97,0624
Non-polymers8604
Water95553
1
1: Human COXSACKIEVIRUS A21
2: Human COXSACKIEVIRUS A21
3: Human coxsackievirus A21
4: Human coxsackievirus A21
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,875,347480
Polymers5,823,745240
Non-polymers51,602240
Water3,243180
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
1: Human COXSACKIEVIRUS A21
2: Human COXSACKIEVIRUS A21
3: Human coxsackievirus A21
4: Human coxsackievirus A21
hetero molecules
x 5


  • icosahedral pentamer
  • 490 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)489,61240
Polymers485,31220
Non-polymers4,30020
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Human COXSACKIEVIRUS A21
2: Human COXSACKIEVIRUS A21
3: Human coxsackievirus A21
4: Human coxsackievirus A21
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 588 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)587,53548
Polymers582,37424
Non-polymers5,16024
Water32418
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
6
1: Human COXSACKIEVIRUS A21
2: Human COXSACKIEVIRUS A21
3: Human coxsackievirus A21
4: Human coxsackievirus A21
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 490 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)489,61240
Polymers485,31220
Non-polymers4,30020
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)348.014, 348.014, 348.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)
3generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)
4generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)
5generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)

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Components

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Human COXSACKIEVIRUS ... , 4 types, 4 molecules 1234

#1: Protein Human COXSACKIEVIRUS A21


Mass: 33264.262 Da / Num. of mol.: 1 / Fragment: Viral Protein 1 / 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: UniProt: Q71LY2, UniProt: P22055*PLUS
#2: Protein Human COXSACKIEVIRUS A21


Mass: 29918.537 Da / Num. of mol.: 1 / Fragment: Viral Protein 2 / 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: UniProt: Q71LY2, UniProt: P22055*PLUS
#3: Protein Human coxsackievirus A21


Mass: 26568.689 Da / Num. of mol.: 1 / Fragment: Viral Protein 3 / 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: UniProt: Q71LY2, UniProt: P22055*PLUS
#4: Protein Human coxsackievirus A21


Mass: 7310.922 Da / Num. of mol.: 1 / Fragment: Viral Protein 4 / 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: UniProt: Q71LY2, UniProt: P22055*PLUS

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Non-polymers , 4 types, 57 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#7: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.551.2
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop6.4sodium chloride, citrate, glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop6.4sodium chloride, citrate, glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 110120 / Num. obs: 106927 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 17 % / Rmerge(I) obs: 0.119
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 11 % / Rmerge(I) obs: 0.238 / % possible all: 88.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SnBOF DPS SUITEphasing
ENVELOPEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.72 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 17050733.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 11161 10 %RANDOM
Rwork0.224 ---
all0.225 ---
obs0.224 111200 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.6012 Å2 / ksol: 3.60356 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 40 53 6765
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.52
X-RAY DIFFRACTIONc_scangle_it3.82.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 1666 9.8 %
Rwork0.326 15257 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMION.TOP
X-RAY DIFFRACTION5ION.PARAMCARBOHYDRATE.TOP

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