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- PDB-2vrs: Structure of avian reovirus sigmaC117-326, C2 crystal form -

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Basic information

Entry
Database: PDB / ID: 2vrs
TitleStructure of avian reovirus sigmaC117-326, C2 crystal form
ComponentsSIGMA-C CAPSID PROTEIN
KeywordsVIRAL PROTEIN / ALPHA-HELICAL COILED COIL / RECEPTOR-BINDING / TRIPLE BETA-SPIRAL / VIRION / COILED COIL / BETA-BARREL
Function / homology
Function and homology information


viral capsid / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) - #40 / Reovirus sigma C capsid protein, C-terminal / Reovirus sigma C capsid protein triple beta spiral / Reovirus sigma C capsid protein C-terminal domain / Reovirus sigma C capsid protein triple beta spiral / reovirus attachment protein sigma1; domain 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Laminin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) - #40 / Reovirus sigma C capsid protein, C-terminal / Reovirus sigma C capsid protein triple beta spiral / Reovirus sigma C capsid protein C-terminal domain / Reovirus sigma C capsid protein triple beta spiral / reovirus attachment protein sigma1; domain 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Laminin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribbon / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Sigma-C capsid protein
Similarity search - Component
Biological speciesAVIAN REOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGuardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / Benavente, J. / van Raaij, M.J.
Citation
Journal: J. Gen. Virol. / Year: 2009
Title: Crystallographic structure of the alpha-helical triple coiled-coil domain of avian reovirus S1133 fibre.
Authors: Guardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / van Raaij, M.J.
#1: Journal: Acta Crystallogr., Sect.F / Year: 2005
Title: Crystallization of the C-Terminal Globular Domain of Avian Reovirus Fibre.
Authors: van Raaij, M.J. / Hermo-Parrado, X.L. / Guardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / Costas, C. / Martinez-Costas, J. / Benavente, J.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Structure of the Carboxy-Terminal Receptor-Binding Domain of Avian Reovirus Fibre Sigmac.
Authors: Guardado-Calvo, P. / Fox, G.C. / Hermo-Parrado, X.L. / Llamas-Saiz, A.L. / Costas, C. / Martinez-Costas, J. / Benavente, J. / van Raaij, M.J.
History
DepositionApr 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC", "CB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC", "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGMA-C CAPSID PROTEIN
B: SIGMA-C CAPSID PROTEIN
C: SIGMA-C CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,66216
Polymers67,7613
Non-polymers90113
Water17,565975
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-100.4 kcal/mol
Surface area32370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)142.789, 54.008, 121.336
Angle α, β, γ (deg.)90.00, 101.79, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.43565, -0.84714, -0.30422), (0.84761, -0.49985, 0.17808), (-0.30293, -0.18028, 0.93581)87.71729, -9.05331, 18.75791
2given(-0.44441, -0.84035, -0.31035), (0.8387, -0.51203, 0.18548), (-0.31478, -0.17786, 0.93235)88.23477, -8.91559, 19.02875
3given(-0.42461, -0.8556, -0.29605), (0.85249, -0.48795, 0.18751), (-0.30489, -0.17277, 0.93659)87.04472, -9.97376, 18.28341

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein SIGMA-C CAPSID PROTEIN / SIGMA-3 PROTEIN / SIGMA C


Mass: 22587.023 Da / Num. of mol.: 3 / Fragment: RESIDUES 117-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN REOVIRUS / Strain: S1133
Description: THE AVIAN REOVIRUS STRAIN S1133 WAS ORIGINALLY PROVIDED BY DR. PHILIP I.MARCUS WHEN DR. J.BENAVENTE WAS A ROCHE VISITING SCIENTIST IN THE LABORATORY OF DR. A.SHATKIN
Plasmid: PET28C-PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q992I2

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Non-polymers , 5 types, 988 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE FIRST RESIDUE, ILE-116, IS A REMNANT OF THE EXPRESSION TAG.

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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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 8.4
Details: 0.6-0.75 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.4, 25% GLYCEROL, 50 MM ZINC SULPHATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.8266
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 3, 2007 / Details: RD COATED FLAT AND TOROIDAL MIRRORS
RadiationMonochromator: SI111 DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 90954 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BSF

2bsf


Resolution: 1.75→18.43 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.051 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 117-121 OF CHAIN A AND CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1738 1.9 %THIN SHELLS
Rwork0.18 ---
obs0.18 89213 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å2-0.43 Å2
2--0.24 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 1.75→18.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 32 975 5653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214765
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9476467
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62323.418196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43715730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3921533
X-RAY DIFFRACTIONr_chiral_restr0.1140.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023582
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.22168
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.23369
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2735
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.04953154
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.1674987
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.727101796
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.967151480
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.87 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.278 329
Rwork0.234 15852

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