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- PDB-4gb3: Human coxsackievirus B3 strain RD coat protein -

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Basic information

Entry
Database: PDB / ID: 4gb3
TitleHuman coxsackievirus B3 strain RD coat protein
Components(coat protein ...) x 4
KeywordsVIRUS / Capsid Protein
Function / homology
Function and homology information


: / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 RIG-I 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 / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / 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
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsYoder, J.D. / Hafenstein, S.
CitationJournal: J Virol / Year: 2012
Title: The crystal structure of a coxsackievirus B3-RD variant and a refined 9-angstrom cryo-electron microscopy reconstruction of the virus complexed with decay-accelerating factor (DAF) provide a ...Title: The crystal structure of a coxsackievirus B3-RD variant and a refined 9-angstrom cryo-electron microscopy reconstruction of the virus complexed with decay-accelerating factor (DAF) provide a new footprint of DAF on the virus surface.
Authors: Joshua D Yoder / Javier O Cifuente / Jieyan Pan / Jeffrey M Bergelson / Susan Hafenstein /
Abstract: The coxsackievirus-adenovirus receptor (CAR) and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). The first described DAF-binding isolate was ...The coxsackievirus-adenovirus receptor (CAR) and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). The first described DAF-binding isolate was obtained during passage of the prototype strain, Nancy, on rhabdomyosarcoma (RD) cells, which express DAF but very little CAR. Here, the structure of the resulting variant, CVB3-RD, has been solved by X-ray crystallography to 2.74 Å, and a cryo-electron microscopy reconstruction of CVB3-RD complexed with DAF has been refined to 9.0 Å. This new high-resolution structure permits us to correct an error in our previous view of DAF-virus interactions, providing a new footprint of DAF that bridges two adjacent protomers. The contact sites between the virus and DAF clearly encompass CVB3-RD residues recently shown to be required for binding to DAF; these residues interact with DAF short consensus repeat 2 (SCR2), which is known to be essential for virus binding. Based on the new structure, the mode of the DAF interaction with CVB3 differs significantly from the mode reported previously for DAF binding to echoviruses.
History
DepositionJul 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: coat protein 1
2: coat protein 2
3: coat protein 3
4: coat protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2886
Polymers93,8034
Non-polymers4852
Water00
1
1: coat protein 1
2: coat protein 2
3: coat protein 3
4: coat protein 4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,657,292360
Polymers5,628,205240
Non-polymers29,088120
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: coat protein 1
2: coat protein 2
3: coat protein 3
4: coat protein 4
hetero molecules
x 5


  • icosahedral pentamer
  • 471 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)471,44130
Polymers469,01720
Non-polymers2,42410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: coat protein 1
2: coat protein 2
3: coat protein 3
4: coat protein 4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 566 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)565,72936
Polymers562,82024
Non-polymers2,90912
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: coat protein 1
2: coat protein 2
3: coat protein 3
4: coat protein 4
hetero molecules
x 10


  • crystal asymmetric unit, crystal frame
  • 943 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)942,88260
Polymers938,03440
Non-polymers4,84820
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)296.638, 296.638, 813.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(1), (1), (1)
2generate(0.50027, -0.6448, 0.5779), (0.86587, 0.3729, -0.33349), (-0.00046, 0.66722, 0.74486)-175.7482, 272.88557, 11.94664
3generate(0.50027, 0.86587, -0.00046), (-0.6448, 0.3729, 0.66722), (0.5779, -0.33349, 0.74486)-148.35623, -223.05168, 183.67136
4generate(0.31062, -0.17742, 0.93383), (-0.17742, -0.97598, -0.12641), (0.93383, -0.12641, -0.33464)-340.27258, 176.64576, 511.13326
5generate(0.80945, -0.10862, 0.57705), (0.4675, -0.47541, -0.74527), (0.35529, 0.87303, -0.33404)-175.26457, 397.44294, 339.32657
6generate(0.80945, 0.4675, 0.35529), (-0.10862, -0.47541, 0.87303), (0.57705, -0.74527, -0.33404)-164.49522, -126.33252, 510.68984
7generate(0.30882, 0.75673, 0.57619), (0.75673, -0.56248, 0.33314), (0.57619, 0.33314, -0.74634)-323.60126, 156.17395, 529.96207
8generate(0.80846, 0.10973, -0.57823), (0.46794, 0.47605, 0.74459), (0.35697, -0.87254, 0.33352)118.54512, -86.96464, 308.12413
9generate(0.00134, -0.93377, 0.35786), (0.35662, -0.33389, -0.87255), (0.93425, 0.12879, 0.33255)-165.8693, 403.26407, 308.84274
10generate(0.80957, -0.46639, -0.35647), (-0.11055, 0.47526, -0.87287), (0.57652, 0.74606, 0.3332)107.94119, 264.57081, 202.59464

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Components

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Coat protein ... , 4 types, 4 molecules 1234

#1: Protein coat protein 1


Mass: 31364.068 Da / Num. of mol.: 1 / Fragment: UNP residues 571-851 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus B3 / Strain: RD / References: UniProt: F8VA14
#2: Protein coat protein 2


Mass: 28878.580 Da / Num. of mol.: 1 / Fragment: UNP residues 70-332 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus B3 / Strain: RD / References: UniProt: F8VA14
#3: Protein coat protein 3


Mass: 26211.725 Da / Num. of mol.: 1 / Fragment: UNP residues 333-570 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus B3 / Strain: RD / References: UniProt: F8VA14
#4: Protein coat protein 4


Mass: 7349.039 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) Human coxsackievirus B3 / Strain: RD / References: UniProt: F8VA14

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 298 K / pH: 6
Details: 2 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2008
RadiationMonochromator: BENT GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.74→15 Å / Num. obs: 343901 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.75
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.97 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COV

1cov


Resolution: 2.74→15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 72829.27 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.339 16562 5 %RANDOM
Rwork0.33 ---
obs0.33 331647 93.2 %-
all-331647 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.1026 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1-9.02 Å2-0 Å20 Å2
2--9.02 Å2-0 Å2
3----18.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.89 Å0.82 Å
Refinement stepCycle: LAST / Resolution: 2.74→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 33 0 6427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
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
LS refinement shellResolution: 2.74→2.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.464 2633 5 %
Rwork0.444 49569 -
obs--88.6 %

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