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- PDB-4cdx: Crystal structure of human Enterovirus 71 in complex with the unc... -

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Basic information

Entry
Database: PDB / ID: 4cdx
TitleCrystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP12
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / HAND-FOOT-AND-MOUTH DISEASE / ENTEROVIRUS UNCOATING / INHIBITOR
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / 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 ...Rhinovirus 14, subunit 4 - #370 / 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. / 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
Chem-JF0 / Genome polyprotein
Similarity search - Component
Biological speciesENTEROVIRUS A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsDe Colibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. ...De Colibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. / Wang, J. / Li, X. / Peng, W. / Rowlands, D. / Fry, E.E. / Rao, Z. / Stuart, D.I.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2014
Title: More-Powerful Virus Inhibitors from Structure-Based Analysis of Hev71 Capsid-Binding Molecules.
Authors: De Colibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. / Wang, J. / Li, X. / Peng, W. / Rowlands, D.J. / ...Authors: De Colibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. / Wang, J. / Li, X. / Peng, W. / Rowlands, D.J. / Fry, E.E. / Rao, Z. / Stuart, D.I.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A Sensor-Adaptor Mechanism for Enterovirus Uncoating from Structures of Ev71.
Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D. ...Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
History
DepositionNov 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8717
Polymers94,4094
Non-polymers4623
Water1,982110
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,692,254420
Polymers5,664,563240
Non-polymers27,690180
Water4,324240
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area2336640 Å2
ΔGint-12403 kcal/mol
Surface area999470 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,35435
Polymers472,04720
Non-polymers2,30815
Water36020
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,22542
Polymers566,45624
Non-polymers2,76918
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
Unit cell
Length a, b, c (Å)599.690, 599.690, 599.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.4686, 0.5824, 0.6642), (-0.1984, 0.6633, -0.7216), (-0.8608, -0.4699, -0.1953)32.1597, 184.166, 369.979
3generate(0.3239, 0.8955, 0.3053), (-0.8082, 0.4297, -0.4027), (-0.4918, -0.1163, 0.8629)-77.129, 260.939, 108.874
4generate(0.3099, 0.734, -0.6044), (-0.7573, 0.5748, 0.3098), (0.5748, 0.3617, 0.734)82.1013, 127.676, -98.1734
5generate(-0.4921, 0.3214, -0.809), (-0.1183, 0.896, 0.428), (0.8625, 0.3063, -0.4029)289.965, -30.2914, 34.4766
6generate(-0.9734, 0.2278, -0.02457), (0.2278, 0.951, -0.2092), (-0.02429, -0.2092, -0.9776)259.086, 4.46497, 324.187
7generate(0.4316, -0.4047, -0.8062), (-0.1171, 0.861, -0.495), (0.8944, 0.308, 0.3242)260.854, 110.082, -77.0713
8generate(-0.4885, -0.7702, -0.4101), (-0.593, 0.6378, -0.4915), (0.6401, 0.003061, -0.7683)390.953, 211.908, 165.128
9generate(-0.4887, -0.5917, 0.6412), (-0.7691, 0.6391, 0.003552), (-0.4118, -0.4914, -0.7674)210.453, 164.819, 391.388
10generate(0.4312, -0.1153, 0.8949), (-0.4021, 0.8633, 0.305), (-0.8077, -0.4913, 0.3259)-31.2158, 33.9347, 288.845
11generate(0.8623, -0.4927, -0.117), (0.3072, 0.3254, 0.8943), (-0.4026, -0.8071, 0.432)109.573, -77.3174, 260.337
12generate(-0.2044, -0.9787, -0.01995), (0.2309, -0.02838, -0.9726), (0.9513, -0.2034, 0.2318)322.764, 259.737, 3.12535
13generate(-0.2046, 0.2327, 0.9508), (-0.9786, -0.02712, -0.204), (-0.02167, -0.9722, 0.2333)2.56546, 323.712, 258.054
14generate(0.7358, 0.5738, 0.3596), (-0.6019, 0.311, 0.7355), (0.3102, -0.7577, 0.5742)-98.1969, 81.064, 127.927
15generate(0.5726, 0.3071, -0.7601), (0.3634, 0.736, 0.5712), (0.7349, -0.6033, 0.3098)129.054, -98.2388, 82.027
16generate(-0.4685, -0.2008, -0.8603), (0.5819, 0.6626, -0.4716), (0.6648, -0.7215, -0.1936)370.695, 33.4565, 183.515
17generate(0.006654, -0.7666, 0.642), (-0.7673, -0.4156, -0.4883), (0.6412, -0.4894, -0.591)163.55, 391.503, 211.13
18generate(0.3243, -0.8093, -0.4897), (0.8951, 0.43, -0.1179), (0.306, -0.4001, 0.8639)289.374, -30.1184, 33.6709
19generate(0.6657, -0.4662, 0.5826), (-0.72, -0.1965, 0.6655), (-0.1958, -0.8626, -0.4665)31.7879, 182.995, 370.108
20generate(-0.9488, -0.2466, 0.1973), (-0.2471, 0.1904, -0.9501), (0.1967, -0.9502, -0.2415)292.416, 294.281, 292.554

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 32699.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0
#2: Protein VP2


Mass: 27740.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0
#3: Protein VP3


Mass: 26468.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0
#4: Protein VP4


Mass: 7501.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0

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Non-polymers , 3 types, 113 molecules

#5: Chemical ChemComp-JF0 / 1-(5-((3'-METHYL-[1,1'-BIPHENYL]-4-YL)OXY)PENTYL)-3-(


Mass: 415.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N3O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 13

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Sample preparation

CrystalDensity % sol: 75 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG400, 0.2 M TRI-SODIUM CITRATE, 0.1 M TRIS.HCL PH 8.5, MIXED WITH VIRUS AND EQUILIBRATED AGAINST SALT RESERVOIR, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2012 / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 583785 / % possible obs: 67.4 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.54 / Net I/σ(I): 1.83
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.57 / % possible all: 66.5

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.3phasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→49.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 69097870.47 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 28128 5 %RANDOM
Rwork0.27 ---
obs0.27 560270 64.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.771 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.45 Å
Luzzati d res low-10 Å
Luzzati sigma a0.54 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 33 110 6649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 2348 4.9 %
Rwork0.363 45629 -
obs--55.5 %
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 DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION6GPP12.PARGPP12.TOP

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