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- PDB-1d4m: THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1d4m
TitleTHE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION
Components(PROTEIN (COXSACKIEVIRUS ...) x 4
KeywordsVIRUS / PICORNAVIRUS STRUCTURE / RGD / UNCOATING / VIRUS-RECEPTOR INTERACTION / WIN COMPOUND / VIRUS/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 / 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 / Few Secondary Structures / Irregular / 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. / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Chem-W71 / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus A9
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsHendry, E. / Hatanaka, H. / Fry, E. / Smyth, M. / Tate, J. / Stanway, G. / Santti, J. / Maaronen, M. / Hyypia, T. / Stuart, D.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses.
Authors: Hendry, E. / Hatanaka, H. / Fry, E. / Smyth, M. / Tate, J. / Stanway, G. / Santti, J. / Maaronen, M. / Hyypia, T. / Stuart, D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Analysis of Coxsackievirus A9
Authors: Smyth, M. / Hall, J. / Fry, E. / Stuart, D. / Stanway, G. / Hyypia, T.
History
DepositionOct 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 31, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_oper_list ...database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: PROTEIN (COXSACKIEVIRUS A9)
2: PROTEIN (COXSACKIEVIRUS A9)
3: PROTEIN (COXSACKIEVIRUS A9)
4: PROTEIN (COXSACKIEVIRUS A9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3557
Polymers96,4424
Non-polymers9133
Water8,071448
1
1: PROTEIN (COXSACKIEVIRUS A9)
2: PROTEIN (COXSACKIEVIRUS A9)
3: PROTEIN (COXSACKIEVIRUS A9)
4: PROTEIN (COXSACKIEVIRUS A9)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,841,293420
Polymers5,786,499240
Non-polymers54,794180
Water4,324240
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: PROTEIN (COXSACKIEVIRUS A9)
2: PROTEIN (COXSACKIEVIRUS A9)
3: PROTEIN (COXSACKIEVIRUS A9)
4: PROTEIN (COXSACKIEVIRUS A9)
hetero molecules
x 5


  • icosahedral pentamer
  • 487 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)486,77435
Polymers482,20820
Non-polymers4,56615
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: PROTEIN (COXSACKIEVIRUS A9)
2: PROTEIN (COXSACKIEVIRUS A9)
3: PROTEIN (COXSACKIEVIRUS A9)
4: PROTEIN (COXSACKIEVIRUS A9)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 584 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)584,12942
Polymers578,65024
Non-polymers5,47918
Water43224
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: PROTEIN (COXSACKIEVIRUS A9)
2: PROTEIN (COXSACKIEVIRUS A9)
3: PROTEIN (COXSACKIEVIRUS A9)
4: PROTEIN (COXSACKIEVIRUS A9)
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.92 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,920,647210
Polymers2,893,249120
Non-polymers27,39790
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)487.300, 358.100, 305.700
Angle α, β, γ (deg.)90.00, 128.10, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.33011347, -0.93642557, -0.11887911), (0.93642557, 0.30901699, 0.16617954), (-0.11887911, -0.16617954, 0.97890353)
3generate(-0.75378571, -0.57874283, -0.31122955), (0.57874283, -0.80901699, 0.10270461), (-0.31122955, -0.10270461, 0.94476872)
4generate(-0.75378571, 0.57874283, -0.31122955), (-0.57874283, -0.80901699, -0.10270461), (-0.31122955, 0.10270461, 0.94476872)
5generate(0.33011347, 0.93642557, -0.11887911), (-0.93642557, 0.30901699, -0.16617954), (-0.11887911, 0.16617954, 0.97890353)
6generate(-0.80953691, -0.30859609, -0.49941811), (-0.30859609, -0.5, 0.80917764), (-0.49941811, 0.80917764, 0.30953691)
7generate(-0.49684592, 0.7457027, -0.44392748), (-0.66627883, 0.7457027), (0.55607252, 0.66627883, 0.49684592)
8generate(0.58705326, 0.7694657, -0.25157704), (-0.30859609, 0.5, 0.80917764), (0.74842296, -0.39739468, 0.53098073)
9generate(0.9442488, -0.27014675, -0.18818856), (0.27014675, 0.30901699, 0.91188225), (-0.18818856, -0.91188225, 0.36476819)
10generate(0.08110861, -0.93642557, -0.34136276), (0.27014675, -0.30901699, 0.91188225), (-0.95939675, -0.16617954, 0.22790838)
11generate(-0.9442488, -0.27014675, 0.18818856), (-0.27014675, 0.30901699, -0.91188225), (0.18818856, -0.91188225, -0.36476819)
12generate(-0.58705326, 0.7694657, 0.25157704), (0.30859609, 0.5, -0.80917764), (-0.74842296, -0.39739468, -0.53098073)
13generate(0.49684592, 0.7457027, 0.44392748), (0.66627883, -0.7457027), (-0.55607252, 0.66627883, -0.49684592)
14generate(0.80953691, -0.30859609, 0.49941811), (0.30859609, -0.5, -0.80917764), (0.49941811, 0.80917764, -0.30953691)
15generate(-0.08110861, -0.93642557, 0.34136276), (-0.27014675, -0.30901699, -0.91188225), (0.95939675, -0.16617954, -0.22790838)
16generate(0.08110861, -0.27014675, -0.95939675), (0.93642557, -0.30901699, 0.16617954), (-0.34136276, -0.91188225, 0.22790838)
17generate(-0.11214504, -0.99369185), (-1), (-0.99369185, 0.11214504)
18generate(0.08110861, 0.27014675, -0.95939675), (-0.93642557, -0.30901699, -0.16617954), (-0.34136276, 0.91188225, 0.22790838)
19generate(0.3937996, 0.16695987, -0.90390612), (-0.57874283, 0.80901699, -0.10270461), (0.71412787, 0.56357422, 0.4152174)
20generate(0.3937996, -0.16695987, -0.90390612), (0.57874283, 0.80901699, 0.10270461), (0.71412787, -0.56357422, 0.4152174)
21generate(0.49684592, -0.66627883, -0.55607252), (-0.7457027, -0.66627883), (0.44392748, 0.7457027, -0.49684592)
22generate(-0.3937996, -0.57874283, -0.71412787), (-0.16695987, 0.80901699, -0.56357422), (0.90390612, -0.10270461, -0.4152174)
23generate(-0.58705326, 0.30859609, -0.74842296), (0.7694657, 0.5, -0.39739468), (0.25157704, -0.80917764, -0.53098073)
24generate(0.18415494, 0.7694657, -0.61156315), (0.7694657, -0.5, -0.39739468), (-0.61156315, -0.39739468, -0.68415494)
25generate(0.85404147, 0.16695987, -0.49268404), (-0.16695987, -0.80901699, -0.56357422), (-0.49268404, 0.56357422, -0.66305847)
26generate(-0.18415494, 0.7694657, 0.61156315), (-0.7694657, -0.5, 0.39739468), (0.61156315, -0.39739468, 0.68415494)
27generate(0.58705326, 0.30859609, 0.74842296), (-0.7694657, 0.5, 0.39739468), (-0.25157704, -0.80917764, 0.53098073)
28generate(0.3937996, -0.57874283, 0.71412787), (0.16695987, 0.80901699, 0.56357422), (-0.90390612, -0.10270461, 0.4152174)
29generate(-0.49684592, -0.66627883, 0.55607252), (0.7457027, 0.66627883), (-0.44392748, 0.7457027, 0.49684592)
30generate(-0.85404147, 0.16695987, 0.49268404), (0.16695987, -0.80901699, 0.56357422), (0.49268404, 0.56357422, 0.66305847)

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Components

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PROTEIN (COXSACKIEVIRUS ... , 4 types, 4 molecules 1234

#1: Protein PROTEIN (COXSACKIEVIRUS A9)


Mass: 33869.020 Da / Num. of mol.: 1 / Fragment: VP1 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus A9 / Genus: Enterovirus / Species: Human enterovirus B / References: UniProt: P21404
#2: Protein PROTEIN (COXSACKIEVIRUS A9)


Mass: 28885.518 Da / Num. of mol.: 1 / Fragment: VP2 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus A9 / Genus: Enterovirus / Species: Human enterovirus B / References: UniProt: P21404
#3: Protein PROTEIN (COXSACKIEVIRUS A9)


Mass: 26335.072 Da / Num. of mol.: 1 / Fragment: VP3 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus A9 / Genus: Enterovirus / Species: Human enterovirus B / References: UniProt: P21404
#4: Protein PROTEIN (COXSACKIEVIRUS A9)


Mass: 7352.039 Da / Num. of mol.: 1 / Fragment: VP4 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus A9 / Genus: Enterovirus / Species: Human enterovirus B / References: UniProt: P21404

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Non-polymers , 3 types, 451 molecules

#5: Chemical ChemComp-W71 / 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE / COMPOUND IV


Mass: 342.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N2O3
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

Crystal growPH range: 7.6 7.6; 7.6; 7.6
Crystal grow
*PLUS
pH: 7.6 / Method: microdialysis / Details: Smyth, M., (1993) J.Mol.Biol., 230, 667.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium dihydrogen phosphate11
318-26 %(v/v)satammonium sulfate12
2sodium azide11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12901
22901
32901
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSRS PX9.610.87
SYNCHROTRONSRS PX7.221.488
SYNCHROTRONSRS PX9.630.87
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJun 1, 1996
MARRESEARCH2IMAGE PLATEMay 1, 1996
MARRESEARCH3IMAGE PLATEAug 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.4881
ReflectionResolution: 2.9→20 Å / Num. obs: 290000 / % possible obs: 41 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.2
Reflection shellResolution: 2.9→3.1 Å / % possible all: 32
Reflection
*PLUS
Num. measured all: 697000

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.9→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.169 --
obs0.169 290000 41 %
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 65 448 7053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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