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- PDB-5osn: Crystal Structure of Bovine Enterovirus 2 determined with Serial ... -

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Basic information

Entry
Database: PDB / ID: 5osn
TitleCrystal Structure of Bovine Enterovirus 2 determined with Serial Femtosecond X-ray Crystallography
Components(Capsid proteinCapsid) x 4
KeywordsVIRUS / ENTEROVIRUS / PICORNAVIRUS / ICOSAHEDRAL VIRUS / FEMTOSECOND X-RAY CRYSTALLOGRAPHY / X-RAY FREE ELECTRON LASERS
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / symbiont-mediated suppression of host gene expression / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLUTAMIC ACID / : / octyl sulfate / SPHINGOSINE / Capsid protein VP0
Similarity search - Component
Biological speciesEnterovirus E
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoedig, P. / Ginn, H.M. / Pakendorf, T. / Sutton, G. / Harlos, K. / Walter, T.S. / Meyer, J. / Fischer, P. / Duman, R. / Vartiainen, I. ...Roedig, P. / Ginn, H.M. / Pakendorf, T. / Sutton, G. / Harlos, K. / Walter, T.S. / Meyer, J. / Fischer, P. / Duman, R. / Vartiainen, I. / Reime, B. / Warmer, M. / Brewster, A.S. / Young, I.D. / Michels-Clark, T. / Sauter, N.K. / Kotecha, A. / Kelly, J. / Rowlands, D.J. / Sikorsky, M. / Nelson, S. / Damiani, D.S. / Alonso-Mori, R. / Ren, J. / Fry, E.E. / David, C. / Stuart, D.I. / Wagner, A. / Meents, A.
CitationJournal: Nat. Methods / Year: 2017
Title: High-speed fixed-target serial virus crystallography.
Authors: Roedig, P. / Ginn, H.M. / Pakendorf, T. / Sutton, G. / Harlos, K. / Walter, T.S. / Meyer, J. / Fischer, P. / Duman, R. / Vartiainen, I. / Reime, B. / Warmer, M. / Brewster, A.S. / Young, I.D. ...Authors: Roedig, P. / Ginn, H.M. / Pakendorf, T. / Sutton, G. / Harlos, K. / Walter, T.S. / Meyer, J. / Fischer, P. / Duman, R. / Vartiainen, I. / Reime, B. / Warmer, M. / Brewster, A.S. / Young, I.D. / Michels-Clark, T. / Sauter, N.K. / Kotecha, A. / Kelly, J. / Rowlands, D.J. / Sikorsky, M. / Nelson, S. / Damiani, D.S. / Alonso-Mori, R. / Ren, J. / Fry, E.E. / David, C. / Stuart, D.I. / Wagner, A. / Meents, A.
History
DepositionAug 17, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionAug 30, 2017ID: 5MQU
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / refine_ls_restr_ncs / struct_conn / struct_site
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _refine_ls_restr_ncs.pdbx_refine_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 10, 2018Group: Data collection / Structure summary / Category: computing / entity / Item: _entity.formula_weight
Revision 2.2Nov 14, 2018Group: Data collection / Structure summary / Category: diffrn / entity
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight
Revision 2.3Jul 31, 2019Group: Data collection / Refinement description / Category: pdbx_xplor_file / refine / Item: _pdbx_xplor_file.pdbx_refine_id
Revision 2.4Jan 17, 2024Group: 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,70011
Polymers91,8314
Non-polymers8697
Water6,089338
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,562,018660
Polymers5,509,863240
Non-polymers52,156420
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation48
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation12_555-y,-z,x1
Unit cell
Length a, b, c (Å)436.600, 436.600, 436.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1generate(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)

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Capsid protein / Capsid


Mass: 30217.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus E / References: UniProt: Q65480
#2: Protein Capsid protein / Capsid


Mass: 26757.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus E / References: UniProt: Q65480
#3: Protein Capsid protein / Capsid


Mass: 27149.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus E / References: UniProt: Q65480
#4: Protein Capsid protein / Capsid


Mass: 7705.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus E / References: UniProt: Q65480

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Non-polymers , 6 types, 345 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#8: Chemical ChemComp-OSF / octyl sulfate


Mass: 209.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17O4S
#9: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.500 M Ammonium Sulphate 0.100 M Tris

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.305 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 235593 / % possible obs: 82.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.746 / R split: 0.486 / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 2.4 % / % possible all: 83.6

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Processing

Software
NameVersionClassification
CNS1.3refinement
CNS1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEV

1bev


Resolution: 2.3→29.71 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 49218500.33 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. Based on the electron density and local environment, residues LEU 102, HIS 103, ALA 143, ARG 192 and SER 213 of VP3 in UNP Q65480 were identified as PHE, THR, ASN, ...Details: BULK SOLVENT MODEL USED. Based on the electron density and local environment, residues LEU 102, HIS 103, ALA 143, ARG 192 and SER 213 of VP3 in UNP Q65480 were identified as PHE, THR, ASN, ALA and ALA, respectively.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 11604 4.9 %RANDOM
Rwork0.233 ---
obs0.233 235593 78 %-
Solvent computationBsol: 107.958 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: 1 / Resolution: 2.3→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 49 341 6592
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it10.9210
X-RAY DIFFRACTIONc_mcangle_it11.3220
X-RAY DIFFRACTIONc_scbond_it13.9712
X-RAY DIFFRACTIONc_scangle_it15.525
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 1213 4.8 %
Rwork0.326 23846 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top
X-RAY DIFFRACTION6CNS_TOPPAR/../mgl.par../mgl.top
X-RAY DIFFRACTION7../osf.par../osf.top
X-RAY DIFFRACTION8../sph.par../sph.top

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