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- PDB-4gmp: Crystal structure of enterovirus 71 strain 1095 procapsid -

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Basic information

Entry
Database: PDB / ID: 4gmp
TitleCrystal structure of enterovirus 71 strain 1095 procapsid
Components
  • capsid protein VP0
  • capsid protein VP1
  • capsid protein VP3
KeywordsVIRUS / Capsid Protein
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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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) ...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 / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsYoder, J.D. / Hafenstein, S.
CitationJournal: J Virol / Year: 2013
Title: Structures of the procapsid and mature virion of enterovirus 71 strain 1095.
Authors: Javier O Cifuente / Hyunwook Lee / Joshua D Yoder / Kristin L Shingler / Michael S Carnegie / Jennifer L Yoder / Robert E Ashley / Alexander M Makhov / James F Conway / Susan Hafenstein /
Abstract: Enterovirus 71 (EV71) is an important emerging human pathogen with a global distribution and presents a disease pattern resembling poliomyelitis with seasonal epidemics that include cases of severe ...Enterovirus 71 (EV71) is an important emerging human pathogen with a global distribution and presents a disease pattern resembling poliomyelitis with seasonal epidemics that include cases of severe neurological complications, such as acute flaccid paralysis. EV71 is a member of the Picornaviridae family, which consists of icosahedral, nonenveloped, single-stranded RNA viruses. Here we report structures derived from X-ray crystallography and cryoelectron microscopy (cryo-EM) for the 1095 strain of EV71, including a putative precursor in virus assembly, the procapsid, and the mature virus capsid. The cryo-EM map of the procapsid provides new structural information on portions of the capsid proteins VP0 and VP1 that are disordered in the higher-resolution crystal structures. Our structures solved from virus particles in solution are largely in agreement with those from prior X-ray crystallographic studies; however, we observe small but significant structural differences for the 1095 procapsid compared to a structure solved in a previous study (X. Wang, W. Peng, J. Ren, Z. Hu, J. Xu, Z. Lou, X. Li, W. Yin, X. Shen, C. Porta, T. S. Walter, G. Evans, D. Axford, R. Owen, D. J. Rowlands, J. Wang, D. I. Stuart, E. E. Fry, and Z. Rao, Nat. Struct. Mol. Biol. 19:424-429, 2012) for a different strain of EV71. For both EV71 strains, the procapsid is significantly larger in diameter than the mature capsid, unlike in any other picornavirus. Nonetheless, our results demonstrate that picornavirus capsid expansion is possible without RNA encapsidation and that picornavirus assembly may involve an inward radial collapse of the procapsid to yield the native virion.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Feb 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
0: capsid protein VP0
1: capsid protein VP1
3: capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)94,3363
Polymers94,3363
Non-polymers00
Water0
1
0: capsid protein VP0
1: capsid protein VP1
3: capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,660,174180
Polymers5,660,174180
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
0: capsid protein VP0
1: capsid protein VP1
3: capsid protein VP3
x 5


  • icosahedral pentamer
  • 472 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)471,68115
Polymers471,68115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
0: capsid protein VP0
1: capsid protein VP1
3: capsid protein VP3
x 6


  • icosahedral 23 hexamer
  • 566 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)566,01718
Polymers566,01718
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
0: capsid protein VP0
1: capsid protein VP1
3: capsid protein VP3
x 5


  • crystal asymmetric unit, crystal frame
  • 472 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)471,68115
Polymers471,68115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)350.248, 350.248, 350.248
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(1), (1), (1)
2generate(0.30904, 0.50148, 0.8081), (-0.50483, 0.8066, -0.30748), (-0.806, -0.31293, 0.50243)-0.28721, 0.45265, 0.72744
3generate(-0.80904, -0.31543, -0.49595), (0.30648, 0.4936, -0.8139), (0.50152, -0.81047, -0.30267)1.17438, 0.4635, 0.73694
4generate(0.30895, -0.50488, -0.80601), (0.50144, 0.80658, -0.31303), (0.80815, -0.30745, 0.50236)0.90377, 0.00695, 0.00614
5generate(-0.80898, 0.30649, 0.50161), (-0.31547, 0.49367, -0.81041), (-0.49601, -0.81385, -0.30268)0.43827, 0.73905, 1.18281

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Components

#1: Protein capsid protein VP0 / / capsid protein VP2 / capsid protein VP4


Mass: 35223.246 Da / Num. of mol.: 1 / Fragment: UNP residues 1-323 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 71 / Strain: 1095 / References: UniProt: E5RPG0
#2: Protein capsid protein VP1 /


Mass: 32646.758 Da / Num. of mol.: 1 / Fragment: UNP residues 566-862 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 71 / Strain: 1095 / References: UniProt: E5RPG0, UniProt: Q91D09*PLUS
#3: Protein capsid protein VP3 /


Mass: 26466.227 Da / Num. of mol.: 1 / Fragment: UNP residues 324-565 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 71 / Strain: 1095 / References: UniProt: E5RPG0

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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

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4% PEG8000, 0.4% glycerol, 0.6 M sodium chloride, 0.2 M calcium chloride, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2011
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water-cooled Cu block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 66880 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.9→3.97 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→49.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 18777118.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3398 5.1 %RANDOM
Rwork0.269 ---
obs0.269 66880 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 96.0406 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 127.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 3.9→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5395 0 0 0 5395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.06
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.9→4.14 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 549 5 %
Rwork0.338 10373 -
obs-6529 99.9 %
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

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