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- PDB-4q4y: Crystal structure of Coxsackievirus A24v soaked with Disialyllact... -

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Basic information

Entry
Database: PDB / ID: 4q4y
TitleCrystal structure of Coxsackievirus A24v soaked with Disialyllacto-N-tetraose (DSLNT)
Components(Coxsackievirus capsid protein ...) x 4
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 / virion attachment to host cell / structural molecule activity / 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
HEXANE-1,6-DIOL / MYRISTIC ACID / N-acetyl-alpha-neuraminic acid / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,39921
Polymers98,1534
Non-polymers1,24717
Water14,286793
1
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,963,9661260
Polymers5,889,154240
Non-polymers74,8111020
Water4,324240
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 497 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)496,997105
Polymers490,76320
Non-polymers6,23485
Water36020
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 596 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)596,397126
Polymers588,91524
Non-polymers7,481102
Water43224
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
6
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.49 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,490,991315
Polymers1,472,28960
Non-polymers18,703255
Water1,08160
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation15
Unit cell
Length a, b, c (Å)304.479, 365.298, 366.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.498519, -0.809142, 0.311076), (0.811357, 0.309153, -0.49611), (0.305254, 0.499713, 0.810621)167.0274, 92.88348, -102.83194
3generate(-0.307408, -0.499119, 0.810173), (0.501664, -0.808478, -0.307727), (0.8086, 0.311837, 0.498923)141.47572, 309.97922, -87.99769
4generate(-0.307274, 0.498841, 0.810395), (-0.502244, -0.808341, 0.307143), (0.808291, -0.312639, 0.498922)-40.87979, 350.85114, 26.11822
5generate(0.497648, 0.809893, 0.310514), (-0.811376, 0.308114, 0.496724), (0.306619, -0.499137, 0.810461)-128.32106, 159.5112, 79.25271
6generate(0.307175, -0.499527, 0.81001), (-0.498242, -0.809599, -0.310329), (0.810801, -0.308256, -0.497574)48.31558, 463.20743, 206.82339
7generate(0.000744, -0.001057, 0.999999), (-0.999999, 0.000909, 0.000745), (-0.000909, -0.999999, -0.001056)-31.00996, 334.4855, 366.38333
8generate(0.305506, 0.50132, 0.809534), (-0.500458, 0.807822, -0.311394), (-0.810066, -0.310005, 0.497684)-133.95535, 168.66525, 272.35361
9generate(0.809299, 0.309822, 0.499045), (0.307819, 0.499896, -0.809538), (-0.500283, 0.808774, 0.309196)-118.96106, 192.96585, 55.03659
10generate(0.809031, -0.310094, 0.49931), (0.308318, -0.49935, -0.809685), (0.500409, 0.809006, -0.308382)-5.73815, 375.3884, 15.71982
11generate(-0.501479, 0.808411, 0.308205), (-0.809274, -0.312339, -0.497513), (-0.305931, -0.498914, 0.810858)24.71889, 453.83295, 171.81325
12generate(0.500963, 0.808436, -0.308978), (-0.809592, 0.311539, -0.497497), (-0.305936, 0.499374, 0.810573)-15.14831, 339.95844, -10.40609
13generate(0.809669, -0.309922, -0.498382), (-0.306237, 0.501318, -0.809258), (0.500655, 0.807854, 0.310993)176.57463, 285.89584, -97.89156
14generate(-0.000737, -1, -0.000535), (-0.002148, 0.000536, -0.999998), (0.999997, -0.000736, -0.002149)335.21591, 366.44211, 31.63875
15generate(-0.810162, -0.310498, 0.497221), (-0.30446, -0.501953, -0.809535), (0.50094, -0.807239, 0.312129)241.69281, 468.78473, 196.64314

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Components

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Coxsackievirus capsid protein ... , 4 types, 4 molecules 1234

#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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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 809 molecules

#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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


Mass: 18.015 Da / Num. of mol.: 793 / 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: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM Magnesium chloride, 3.4 M 1,6-Hexanediol, 100 mM HEPES pH 7.5, 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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2012
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.88→49.78 Å / Num. all: 1626655 / Num. obs: 1552490 / % possible obs: 95.4 % / Observed criterion σ(F): -3 / 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: 1.88→49.78 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 2.084 / SU ML: 0.058 / ESU R: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.15652 --
obs0.15652 1552477 95.44 %
all-1626655 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2---0.46 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.88→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6523 0 56 793 7372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026835
X-RAY DIFFRACTIONr_bond_other_d0.0010.026255
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9559310
X-RAY DIFFRACTIONr_angle_other_deg0.73314438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9055859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10323.857293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.519151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3511535
X-RAY DIFFRACTIONr_chiral_restr0.0690.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021580
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_it1.6386.033381
X-RAY DIFFRACTIONr_mcbond_other1.6366.0273380
X-RAY DIFFRACTIONr_mcangle_it2.0577.5954207
X-RAY DIFFRACTIONr_mcangle_other2.0917.9424208
X-RAY DIFFRACTIONr_scbond_it2.5776.6563454
X-RAY DIFFRACTIONr_scbond_other2.6116.9333451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7558.5535090
X-RAY DIFFRACTIONr_long_range_B_refined5.61113.7648246
X-RAY DIFFRACTIONr_long_range_B_other5.21913.4387812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.312 86502 -
Rfree-0 -
obs--72.25 %

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