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- PDB-4iv3: Crystal structure of recombinant foot-and-mouth-disease virus A22... -

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Basic information

Entry
Database: PDB / ID: 4iv3
TitleCrystal structure of recombinant foot-and-mouth-disease virus A22-H2093C empty capsid
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / ICOSAHEDRAL VIRUS / CAPSIDS / PICORNAVIRUS / APTHOVIRUS / VACCINE
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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. / 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
Biological speciesFoot-and-mouth disease virus - type A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPorta, C. / Kotecha, A. / Burman, A. / Jackson, T. / Ren, J. / Loureiro, S. / Jones, I.M. / Fry, E.E. / Stuart, D.I. / Charleston, B.
CitationJournal: Plos Pathog. / Year: 2013
Title: Rational engineering of recombinant picornavirus capsids to produce safe, protective vaccine antigen.
Authors: Porta, C. / Kotecha, A. / Burman, A. / Jackson, T. / Ren, J. / Loureiro, S. / Jones, I.M. / Fry, E.E. / Stuart, D.I. / Charleston, B.
History
DepositionJan 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.2Sep 20, 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
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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)80,7164
Polymers80,7164
Non-polymers00
Water1,00956
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)4,842,974240
Polymers4,842,974240
Non-polymers00
Water3,243180
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
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
x 5


  • icosahedral pentamer
  • 404 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)403,58120
Polymers403,58120
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
x 6


  • icosahedral 23 hexamer
  • 484 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)484,29724
Polymers484,29724
Non-polymers00
Water32418
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
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
x 15


  • crystal asymmetric unit, crystal frame
  • 1.21 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,210,74360
Polymers1,210,74360
Non-polymers00
Water81145
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)328.020, 341.490, 363.370
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:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017)
3generate(-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5)
4generate(-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5)
5generate(0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017)
6generate(1), (1), (1)
7generate(0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5)
8generate(0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017)
9generate(0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017)
10generate(0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5)
11generate(1), (1), (1)
12generate(0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017)
13generate(0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017)
14generate(-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017)
15generate(-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017)

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Components

#1: Protein Capsid protein VP1


Mass: 23090.180 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 726-936
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: IRAQ / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6PN23
#2: Protein Capsid protein VP2


Mass: 24602.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 287-504 / Mutation: H93C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: IRAQ / Plasmid: pBG200 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6PN23
#3: Protein Capsid protein VP3


Mass: 24245.127 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 505-725
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: IRAQ / Plasmid: pBG200 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6PN23
#4: Protein Capsid protein VP4


Mass: 8778.129 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 201-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: IRAQ / Plasmid: pBG200 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6PN23
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 77

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4 M ammonium acetate, 100 mM bis-Tris Propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 353968 / % possible obs: 79.7 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.407 / Net I/σ(I): 2.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 0.7 / Num. unique all: 23484 / % possible all: 53.2

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Processing

Software
NameClassification
GDAdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GH4

4gh4


Resolution: 2.9→49.56 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 18170930.85 / 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
Rfree0.239 17689 5 %RANDOM
Rwork0.235 ---
obs0.235 352479 79.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.229 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.39 Å
Luzzati d res low-6 Å
Luzzati sigma a0.55 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 0 56 4848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.628
X-RAY DIFFRACTIONc_mcangle_it11.3416
X-RAY DIFFRACTIONc_scbond_it13.7312
X-RAY DIFFRACTIONc_scangle_it15.6920
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.362 1124 5.1 %
Rwork0.346 21117 -
obs--50.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION5ion.param
X-RAY DIFFRACTION3ion.top

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