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- PDB-4q4v: Crystal structure of Coxsackievirus A24v -

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Basic information

Entry
Database: PDB / ID: 4q4v
TitleCrystal structure of Coxsackievirus A24v
Components
  • Coxsackievirus capsid protein VP1
  • Coxsackievirus capsid protein VP2
  • Coxsackievirus capsid protein VP3
  • Coxsackievirus capsid protein VP4
KeywordsVIRUS / Coxsackievirus A24v
Function / homology
Function and homology information


: / 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 / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...: / 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 / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / 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 / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / metal ion binding
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) / 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. / 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
Biological speciesCoxsackievirus A24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZocher, G. / Stehle, T.
CitationJournal: Plos Pathog. / Year: 2014
Title: A sialic Acid binding site in a human picornavirus.
Authors: Zocher, G. / Mistry, N. / Frank, M. / Hahnlein-Schick, I. / Ekstrom, J.O. / Arnberg, N. / Stehle, T.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)98,1534
Polymers98,1534
Non-polymers00
Water0
1
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,889,154240
Polymers5,889,154240
Non-polymers00
Water0
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: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
x 5


  • icosahedral pentamer
  • 491 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)490,76320
Polymers490,76320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
x 6


  • icosahedral 23 hexamer
  • 589 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)588,91524
Polymers588,91524
Non-polymers00
Water0
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: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
x 30


  • crystal asymmetric unit, crystal frame
  • 2.94 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,944,577120
Polymers2,944,577120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)303.259, 303.259, 763.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.727622, -0.658474, -0.192295), (0.17448, 0.448755, -0.876456), (0.663417, 0.604177, 0.441415)44.23293, 122.91179, 47.585
3generate(0.288836, -0.891095, 0.350033), (-0.377824, -0.442036, -0.813544), (0.879672, 0.10273, -0.464353)-13.27866, 143.79961, 172.00793
4generate(0.287509, -0.3779, 0.880074), (-0.891502, -0.441458, 0.101682), (0.350091, -0.813822, -0.463821)-93.32326, 34.06599, 201.45073
5generate(0.728201, 0.17395, 0.662921), (-0.657835, 0.448782, 0.604854), (-0.192292, -0.876548, 0.441234)-85.04561, -54.72694, 95.21706
6generate(-0.256842, -0.386699, 0.885718), (-0.696253, 0.709637, 0.107923), (-0.670272, -0.588965, -0.451505)-208.49535, -103.58657, -51.62297
7generate(0.333816, 0.530643, 0.779092), (-0.31143, 0.842176, -0.440172), (-0.889707, -0.095696, 0.44639)-225.14915, -42.09926, -175.10587
8generate(0.851619, 0.48981, -0.186631), (-0.37301, 0.316174, -0.872294), (-0.36825, 0.812478, 0.451964)-108.16881, 26.56043, -205.00529
9generate(0.580594, -0.451691, -0.677411), (-0.795952, -0.139754, -0.589006), (0.171378, 0.881161, -0.440665)-19.30536, 7.2316, -100.35131
10generate(-0.10623, -0.994231, -0.014808), (-0.994241, 0.105996, 0.01583), (-0.014169, 0.016404, -0.999765)-81.43477, -73.17492, -5.50695
11generate(-0.259224, -0.695066, -0.670587), (-0.385013, 0.711135, -0.588262), (0.885758, 0.105693, -0.451952)-160.69849, -37.33165, 172.56532
12generate(-0.75329, -0.547513, 0.364395), (-0.547686, 0.215457, -0.808466), (0.364134, -0.808584, -0.462168)-289.28232, 4.97777, 203.27701
13generate(-0.400619, 0.468191, 0.787592), (-0.897955, -0.029732, -0.439082), (-0.182158, -0.883127, 0.432325)-372.33258, -31.51473, 98.35691
14generate(0.31132, 0.950221, 0.012663), (-0.950304, 0.311269, 0.005837), (0.001605, -0.013851, 0.999903)-295.12927, -95.77781, 2.41485
15generate(0.398757, 0.230463, -0.887626), (-0.633584, 0.768994, -0.08497), (0.662996, 0.596268, 0.45266)-164.29498, -99.48025, 48.54252
16generate(-0.571975, -0.246436, 0.782377), (-0.250017, -0.856042, -0.45242), (0.78124, -0.45438, 0.428021)-296.92145, 235.44679, 237.31442
17generate(0.061388, 0.737275, 0.672798), (-0.628478, -0.495109, 0.599902), (0.775401, -0.459666, 0.432968)-315.06982, 98.0833, 236.89899
18generate(0.620412, 0.696286, -0.360934), (-0.1457, 0.554529, 0.81931), (0.770623, -0.455722, 0.445486)-189.6703, 38.03237, 235.22017
19generate(0.330507, -0.309492, -0.891616), (0.531653, 0.841611, -0.09506), (0.779814, -0.442612, 0.442701)-94.39883, 138.26794, 235.16534
20generate(-0.405042, -0.895545, -0.18423), (0.468823, -0.03044, -0.882768), (0.78495, -0.443929, 0.432181)-160.28226, 260.52399, 236.49268
21generate(-0.207258, -0.414723, -0.88603), (0.962589, -0.248046, -0.109064), (-0.174545, -0.875487, 0.450617)-192.79515, 399.63589, 98.89408
22generate(-0.810468, -0.58562, 0.0138), (0.585412, -0.810568, -0.016502), (0.02085, -0.005296, 0.999769)-295.05853, 406.60394, 5.19111
23generate(-0.681737, 0.278137, 0.676664), (0.275219, -0.759471, 0.589456), (0.677857, 0.588084, 0.441211)-402.0759, 332.34259, 53.12013
24generate(0.002193, 0.982018, 0.188776), (0.460929, -0.16852, 0.871289), (0.887434, 0.085101, -0.45301)-365.90479, 279.82306, 176.23776
25generate(0.294753, 0.553487, -0.778957), (0.884202, 0.151146, 0.441974), (0.362363, -0.819028, -0.444843)-236.52774, 320.80563, 204.59824
26generate(0.937069, 0.302618, 0.174137), (-0.005903, -0.484951, 0.874522), (0.349094, -0.820515, -0.452646)-60.55017, 229.67551, 202.27487
27generate(0.849892, -0.375413, -0.369795), (0.492042, 0.31417, 0.811906), (-0.188622, -0.871988, 0.451729)26.37949, 211.55579, 95.50577
28generate(0.308381, -0.951262, 0.001649), (0.951187, 0.308334, -0.013145), (0.011996, 0.005622, 0.999912)0.3462, 310.57153, 1.71858
29generate(0.060259, -0.629794, 0.774421), (0.736758, -0.495385, -0.460198), (0.673467, 0.598292, 0.434154)-102.64793, 389.87964, 50.58395
30generate(0.449712, 0.144841, 0.881351), (0.145644, -0.985448, 0.087633), (0.881219, 0.088954, -0.464263)-140.1749, 339.95917, 174.4095

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Components

#1: Protein Coxsackievirus capsid protein VP1


Mass: 34378.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3
#2: Protein Coxsackievirus capsid protein VP2


Mass: 29817.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3
#3: Protein Coxsackievirus capsid protein VP3


Mass: 26637.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3
#4: Protein Coxsackievirus capsid protein VP4


Mass: 7319.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 277 K / pH: 4.5
Details: 20mM Calcium chloride, 100mM Sodium acetate, 30% (w/v) MPD, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→99.26 Å / Num. obs: 826150 / % possible obs: 92.7 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
ISPyBdata collection
PYMOLmodel building
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PYMOLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→99.26 Å / Cor.coef. Fo:Fc: 0.929 / SU B: 13.845 / SU ML: 0.235 / ESU R: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.189 --
obs0.189 826125 92.7 %
all-891206 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å2-0 Å2
2--0.23 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.9→99.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6549 0 0 0 6549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.026760
X-RAY DIFFRACTIONr_bond_other_d0.0010.026203
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.959236
X-RAY DIFFRACTIONr_angle_other_deg0.708314305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13523.767292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.565151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2551536
X-RAY DIFFRACTIONr_chiral_restr0.0610.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7899.8523365
X-RAY DIFFRACTIONr_mcbond_other2.7899.853364
X-RAY DIFFRACTIONr_mcangle_it4.26314.7874201
X-RAY DIFFRACTIONr_mcangle_other4.30914.794202
X-RAY DIFFRACTIONr_scbond_it3.40810.2133395
X-RAY DIFFRACTIONr_scbond_other3.43910.2173396
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.02215.1485029
X-RAY DIFFRACTIONr_long_range_B_refined6.25625.2857096
X-RAY DIFFRACTIONr_long_range_B_other6.25625.2877097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.348 40507 -
Rfree-0 -
obs--61.78 %

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