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- PDB-4q4x: Crystal structure of Coxsackievirus A24v soaked with 6'-Sialyllac... -

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Basic information

Entry
Database: PDB / ID: 4q4x
TitleCrystal structure of Coxsackievirus A24v soaked with 6'-Sialyllactose (6SL)
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 / 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
HEXANE-1,6-DIOL / N-acetyl-alpha-neuraminic acid / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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_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.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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)99,09918
Polymers98,1534
Non-polymers94614
Water14,088782
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)5,945,9301080
Polymers5,889,154240
Non-polymers56,776840
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: 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
  • 495 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)495,49490
Polymers490,76320
Non-polymers4,73170
Water36020
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
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 595 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)594,593108
Polymers588,91524
Non-polymers5,67884
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: 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)1,486,483270
Polymers1,472,28960
Non-polymers14,194210
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)306.398, 366.096, 367.700
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(0.498803, 0.809523, 0.309625), (-0.810132, 0.308511, 0.498505), (0.308029, -0.499493, 0.809707)-128.32948, 159.39018, 79.23991
3generate(0.499473, -0.809027, 0.309842), (0.809919, 0.309118, -0.498475), (0.307502, 0.499921, 0.809643)167.81232, 93.7661, -103.57428
4generate(-0.308694, -0.499642, 0.809361), (0.500461, -0.80893, -0.308498), (0.808855, 0.309823, 0.499764)143.13286, 311.1153, -88.63071
5generate(-0.308418, 0.499589, 0.809499), (-0.501038, -0.808689, 0.308193), (0.808603, -0.310538, 0.499728)-39.93013, 351.44739, 25.01546
6generate(0.308066, -0.499633, 0.809606), (-0.498982, -0.809407, -0.30964), (0.810007, -0.308589, -0.498659)48.69485, 464.61093, 207.65131
7generate(4.8E-5, -0.000438, 1), (-1, 0.000645, 4.8E-5), (-0.000645, -1, -0.000438)-30.54585, 336.13715, 367.22433
8generate(0.307088, 0.500736, 0.809296), (-0.500471, 0.808273, -0.310198), (-0.80946, -0.309771, 0.498815)-134.15482, 168.95883, 273.09174
9generate(0.80908, 0.309193, 0.499789), (0.308774, 0.499942, -0.809145), (-0.500048, 0.808985, 0.309023)-119.21421, 192.99768, 55.54319
10generate(0.808894, -0.309484, 0.49991), (0.308969, -0.499644, -0.809255), (0.500229, 0.809058, -0.308538)-5.92183, 376.00131, 15.71297
11generate(0.80905, -0.309837, -0.499438), (-0.307692, 0.500726, -0.809073), (0.500762, 0.808254, 0.309778)177.66666, 287.19205, -98.0384
12generate(-0.00029, -1, -7.4E-5), (-0.000642, 7.4E-5, -1), (1, -0.000289, -0.000642)336.37, 367.09341, 30.79084
13generate(-0.809698, -0.309435, 0.498637), (-0.306995, -0.500808, -0.809287), (0.500143, -0.808357, 0.310508)242.48112, 470.46805, 197.87875
14generate(-0.500585, 0.808771, 0.308712), (-0.809121, -0.310323, -0.499021), (-0.307793, -0.499588, 0.809738)25.15227, 455.49728, 173.39915
15generate(0.500334, 0.808759, -0.309152), (-0.809276, 0.309894, -0.499037), (-0.307796, 0.499874, 0.80956)-14.7315, 341.97739, -9.53395

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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 / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC 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 , 5 types, 795 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / 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: Mar 20, 2013
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 2434133 / Num. obs: 2413465 / % possible obs: 99.2 % / 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: 1.65→49.95 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 1.319 / SU ML: 0.043 / ESU R: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.14879 --
obs0.14879 2413462 99.15 %
all-2434133 -
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: 24.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.19 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 48 782 7339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026866
X-RAY DIFFRACTIONr_bond_other_d0.0010.026286
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9559376
X-RAY DIFFRACTIONr_angle_other_deg0.721314523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8035876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9523.898295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.139151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4171535
X-RAY DIFFRACTIONr_chiral_restr0.0680.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021588
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_it1.2786.0153396
X-RAY DIFFRACTIONr_mcbond_other1.2776.0133395
X-RAY DIFFRACTIONr_mcangle_it1.7597.5834229
X-RAY DIFFRACTIONr_mcangle_other1.7627.5754230
X-RAY DIFFRACTIONr_scbond_it2.1136.5473470
X-RAY DIFFRACTIONr_scbond_other2.1146.5423472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0828.1065125
X-RAY DIFFRACTIONr_long_range_B_refined4.60713.0448308
X-RAY DIFFRACTIONr_long_range_B_other4.2912.7597877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.281 167917 -
Rfree-0 -
obs--93.53 %

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